By Andrew Benson
Hamilton drove a brilliant race in awful conditions at Fuji
The Englishman drove a masterful race in treacherous, wet conditions as his chief rival and McLaren team-mate Fernando Alonso crashed out.
Hamilton leads the Spaniard by 12 points with 20 available in the two remaining races in China and Brazil.
Heikki Kovalainen's Renault was second ahead of the Ferrari of Kimi Raikkonen.
Hamilton's performance, his first wet Grand Prix win, was as controlled and impressive as any he has produced in a scintillating season.
And it means he will win the championship in China next weekend if he beats Alonso, or loses no more than a point to him.
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"It was awful conditions and, in the end, I was fortunate I was able to finish the race after my collision (on lap 34) with Robert Kubica," said the Briton.
"When you're behind, and especially in those conditions, it is the responsibility of the car behind to be extra careful and I felt that it was a risk Robert needn't have taken.
"Still, I got through it and was able to see it home. It felt like the longest race of my life, what with the safety car coming on twice and the conditions being so difficult, but I'm ecstatic to get the victory."
The pouring rain at one point put the entire event in doubt, with conditions so poor that the race was started under the safety car.
And there was immediate controversy when Ferrari started their cars on intermediate tyres rather than the "extreme" wets that had been demanded by race director Charlie Whiting.
Alonso's crash has all but ended his hopes of the championship
Ferrari said they did not know of Whiting's instructions. They claimed they did not receive Whiting's e-mail until after the start of the race, but, as all the other teams received it, it seems more likely that they either did not notice it until then or ignored it.
The team were given the choice to call the cars in to change tyres or be shown the black-and-orange flag that would force them in, and they chose the first option.
It meant the Ferraris were forced to pit with barely two laps gone, a decision Raikkonen said was "unfair".
In the end, the safety car stayed out for 19 laps before Whiting decided the track was safe enough to race on.
It felt like the longest race of my life, what with the safety car coming on twice and the conditions being so difficult
Lewis Hamilton
Alonso, usually outstanding in the wet, came in first, on lap 27, and rejoined in traffic down in seventh place. Hamilton stopped a lap later and came out third.
"It was an unlucky moment," Alonso said. "When I pitted I was behind four cars; when he pitted, he was in front of them."
On new tyres and a heavier fuel load, the two silver cars began to struggle a little, and Hamilton dropped as low as sixth, with Alonso down to 10th, behind rivals who had yet to stop.
Alonso's rear bodywork was damaged when he was hit by Red Bull's Sebastian Vettel and tipped into a spin on his first lap out of the pits.
That will have reduced his car's grip, and the 26-year-old lost control coming out of the tricky and fast Turn Five and smashed into the wall on the entry to Turn Six.
But he refused to blame the damage for the crash: "I aquaplaned and all of a sudden the car was in the wall. I think the aerodynamics were not an important factor."
Kimi was probably quicker than me at everything in the final stages... but I really wanted second so I was prepared to take a few risks
Heikki Kovalainen
But Vettel smashed into the back of Webber while the field was still being controlled, leaving the Australian furious.
Webber was suffering from food poisoning and vomited in his helmet during the first safety-car period, and could not hide his dismay at a potential podium finish being snatched from his grasp.
He swore live on television when first asked about the incident, and later said: "Vettel was a bit wild behind me during the first safety car period and then did a very good job of hitting me very hard under the second safety car.
"I think today he will have learnt a very valuable lesson."
The incident promoted the impressive Kovalainen into second, ahead of Massa, the second Red Bull of David Coulthard and Raikkonen.
Raikkonen passed Coulthard around the outside of Turn Five with 11 laps to go, and that put him just a place behind Massa, who was mathematically out of the title race.
Massa came in for a tyre stop on the next lap, promoting Raikkonen into third place, and ensuring he gained an extra point.
I aquaplaned and all of a sudden the car was in the wall... I think the aerodynamics were not an important factor
Fernando Alonso
The Finn tried hard to pass countryman Kovalainen in the closing laps.
Raikkonen actually passed the Renault on the final lap, but Kovalainen re-passed him immediately and held on to the flag.
"It was a good fight with Kimi," said Kovalainen. "He was probably quicker than me at everything in the final stages and I knew he was really close.
"But I really wanted second so, even though I was aquaplaning at times, I was willing to take a few risks and it meant I could hold on right until the last."
The result leaves Raikkonen 17 points adrift of Hamilton in the championship - still technically within reach, but effectively out of contention unless Hamilton has problems in both remaining races.
Coulthard was fourth, ahead of the Renault of Giancarlo Fisichella, and Massa, who won a no-holds-barred battle with Kubica on the final lap.
Spyker gained their first-ever world championship point after stewards decided that Toro Rosso's Vitantonio Liuzzi had overtaken Adrian Sutil under a yellow flag on lap 55 of Sunday¿s race.
Liuzzi was handed a 25-second penalty, promoting Sutil to eighth overall and denying Toro Rosso their first point of the season.
Englishman Jenson Button's hopes of a strong race after qualifying in a season-best sixth place were dashed when his front wing was broken in a collision at the start of the race.
He rejoined, but was never in the running for points and retired on the last lap with broken suspension following a collision with Super Aguri's Takuma Sato.
Japanese Grand Prix result after 67 laps of Fuji Speedway:
1 Lewis Hamilton (GB) McLaren-Mercedes two hours 0 minutes 34.579seconds
2 Heikki Kovalainen (Fin) Renault 8.377 secs behind
3 Kimi Raikkonen (Fin) Ferrari +9.478secs
4 David Coulthard (GB) Red Bull-Renault +20.297
5 Giancarlo Fisichella (Ita) Renault +38.864
6 Felipe Massa (Brz) Ferrari +49.042
7 Robert Kubica (Pol) BMW Sauber +49.285
8 Adrian Sutil (Ger) Spyker-Ferrari +1:00.129
9 Vitantonio Liuzzi* (Ita) Toro Rosso-Ferrari +1:20.622
10 Rubens Barrichello (Brz) Honda +1:28.342
11 Jenson Button (GB) Honda one lap behind
12 Sakon Yamamoto (Jpn) Spyker-Ferrari one lap
13 Jarno Trulli (Ita) Toyota one Lap
14 Nick Heidfeld (Ger) BMW Sauber two laps
15 Takuma Sato (Jpn) Super Aguri-Honda two laps
R Ralf Schumacher (Ger) Toyota 55 laps completed
R Anthony Davidson (GB) Super Aguri-Honda 54 laps
R Nico Rosberg (Ger) Williams-Toyota 49 laps
R Sebastian Vettel (Ger) Toro Rosso-Ferrari 46 laps
R Mark Webber (Aus) Red Bull-Renault 45 laps
R Fernando Alonso (Spa) McLaren-Mercedes 41 laps
R Alexander Wurz (Aut) Williams 19 laps
* Liuzzi penalised 25 seconds for overtaking while yellow warning flags were being waved
Fuji Speedway
2007 British GP). 

Vodafone McLaren Mercedes driver Lewis Hamilton starting from pole wins the FIA Formula-1 2007 Japanese Grand Prix at the Fuji Speedway, Oyama, Japan. It was the first race on this circuit since 1977, when James Hunt won the race for McLaren-Ford.

A rainy and foggy weekend at Fuji appeared to be very hard for all drivers as the race ran longer then expected and the drivers have to concentrate more due to severe weather conditions. The race started behind the safety car which stayed on a track for an unusually long time, about 40 minutes.

Both Ferrari drivers, who managed to get the second row on the starting grid in the Saturday qualifying session were out of the game on the first laps due to their tyre selection mistake - drivers were forced to change to extreme wet tyres after a few driving errors. When the pace car finally turned off the lights giving the drivers a clear road Hamilton quickly got away from his teammate, Fernando Alonso, who had more fuel on board and thus had a heavier car. Alonso would be eliminated after 41 laps in a driving accident.

Heikki Kovalainen driving for Renault finally leads to a first podium finish for the team in this season, the Finn managed to get second place. On the final laps of the race he masterly defended his position from Kimi Räikkönen, who returned to the battle for podium after the Ferrari start failure.

Sebastian Vettel and Mark Webber both nearly finished on the podium, but a collision between their Toro Rosso and Red Bull sponsored vehicles took them out of the race.

Renault-engined cars did well in the race with David Coulthard and Giancarlo Fisichella finishing in 4th and 5th places.

Robert Kubica got a drive through the pit-lane penalty after some dangerous driving and a collision with Hamilton, causing the Polish driver to be rolled back to 7th place. Felipe Massa took 6th place for Ferrari in his hard battle with Kubica in the sprint to the finish line.

Vitantonio Liuzzi rounded out the top eight for Toro Rosso.

Adrian Sutil did his best for Spyker, finishing ahead of both Hondas. It was confirmed that Spyker will change owners next season becoming the first Indian national Formula One team in history. 

In the Drivers' Championship Hamilton, with 107 points, has increased his lead over teammate Alonso to 12 points. Kimi narrowed the gap to the McLaren drivers, now only five points behind Alonso.