By Phil McNulty
Angry Lille players confront referee Eric Braamhaar
Giggs curled in a quick free-kick after 83 minutes while Lille were still assembling their defensive wall.
Lille players, furious that an earlier header by Peter Odemwingie had been ruled out, walked off the pitch as the last 16 first leg clash boiled over.
They eventually returned, and United held on for a crucial victory.
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United were strengthened by the return of goalkeeper Edwin van der Sar following a broken nose and Wayne Rooney after a domestic suspension.
But the main talking point of a drab first 45 minutes were the worrying scenes involving United's supporters, with too many appearing to be packed in lower tier of the away section.
Dozens of United supporters were concerned, and French police appeared to respond to a genuine security problem by firing off tear gas.
The situation was eventually resolved and the game continued.
United carved out openings near half-time, with Rooney shooting over the top and then seeing another attempt blocked from close range.
The England star burst into life again after 50 minutes, surging past three players - but Giggs was unable to turn in his cross at the far post.
He then set up Ronaldo three minutes later, but Lille keeper Tony Sylva made a crucial block.
Lille were sparked into action, and only Van der Sar's outstretched leg stopped Bodmer from close range.
And there was a highly-debatable incident after 61 minutes when Odemwingie wheeled away in celebration after heading home - but referee Eric Braamhaar ruled the goal out, presumably for a push on Nemanja Vidic.
United boss Ferguson made a subsitution almost immediately, sending on Louis Saha for Ronaldo.
Saha could have made an instant impact, but shot straight at Sylva from only 10 yards.
Henrik Larsson had been quiet, but he almost conjured up a moment of invention to break the deadlock, chipping inches over the bar after Sylva failed to gather Rooney's driven cross.
Lille substitute Johan Audel then turned a good chance over the top as both sides pushed for the winner.
United took the lead with seven minutes left - in an incident that brought the atmosphere inside the ground to boiling point.
Giggs whipped in a 20-yard set-piece as Lille were still organising their defensive wall - and with keeper Sylva scrambling hopelessly out of position.
Lille were furious, and it appeared they were on the point of walking off in protests as several players walked towards the dug-out.
They eventually returned, but even then there were ugly scenes as United's players, including Gary Neville, were pelted with missiles.
But they remained calm and held out comfortably to set the platform for progress in the second leg at Old Trafford.
Lille: Sylva, Chalme, Plestan, Tavlaridis, Tafforeau, Debuchy, Bodmer, Makoun, Obraniak (Michel Bastos 89), Fauvergue (Cabaye 57), Odemwingie (Audel 75).
Subs Not Used: Malicki, Schmitz, Lichtsteiner, Mirallas.
Booked: Fauvergue, Debuchy, Sylva.
Man Utd: Van der Sar, Neville, Ferdinand, Vidic, Evra, Ronaldo (Saha 67), Carrick, Scholes (O'Shea 90), Giggs, Rooney, Larsson.
Subs Not Used: Kuszczak, Brown, Park, Fletcher, Silvestre.
Booked: Evra, Vidic.
Goals: Giggs 83.
Att: 41,000.
Ref: Eric Braamhaar (Holland).
The first leg of the round of sixteen in the  was completed on Wednesday, with at least one controversial result, and a bag full of ties.  The leg began on Tuesday with four games, and the other four were played the next day, including reigning champions FC Barcelona of Spain.

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