Qazi Hussain Ahmed (r) of the MMA boycotted Wednesday's debate
The MMA alliance says its members will resign from national and provincial assemblies after MPs voted that rape should no longer fall under Sharia law.
President Pervez Musharraf in a television speech said the Islamists were isolated on the issue.
The Sharia laws have been widely criticised by human rights groups.
The lower house of the parliament voted overwhelmingly on Wednesday to amend the controversial Sharia law that dates back to 1979.
Until now, rape cases were dealt with in Sharia courts. Victims had to have four male witnesses to the crime - if not, they faced prosecution for adultery.
'US pressure'
Under the amended law, the civil courts will be able to try rape cases according to the British-influenced penal code.
The MMA parties boycotted the vote, saying the bill encouraged "free sex".
They also accuse President Musharraf of pleasing foreign powers.
Women protested outside parliament as the debate was held
In its Thursday meeting in Islamabad, the MMA's supreme council decided that all the alliance's members would resign from the national parliament and provincial assemblies.
Senior MMA leader Liaquat Baloch said this would take place after further meetings on 6 and 7 December.
"They have given free leave to adulterers and fornicators, and those who would spread evil in society," he said.
The MMA found themselves politically isolated by the vote.
Former prime minister Benazir Bhutto's Pakistan People's Party (PPP) voted for the amendment.
Pakistan Muslim League Nawaz (PMLN), led by another former prime minister, Nawaz Sharif, abstained, although it had indicated earlier that it would support the MMA on the issue.
Both the leaders are bitterly opposed to President Musharraf's government and the military's role in politics.
The two parties are partners in the opposition Alliance for Restoration of Democracy (ARD) that seeks to oust the president.
Re-alignment
The ARD and MMA have occasionally joined forces in anti-government campaigns, and both have been working towards a grand anti-Pervez Musharraf alliance.
Hudood laws can punish women for extra-marital sex
But the BBC's M Ilyas Khan says the amendments to the rape laws could drive a wedge between the opposition forces.
Analysts now indicate a re-alignment of political forces ahead of the national elections, expected towards the end of 2007.
Some say the situation, which seemed to be leading to a face-off between the military and the civilian leadership, may now transform into one that pits the Islamists on one side, faced up against the secular political parties and President Musharraf, who argues for a goal of moderate Islam.
But others discount chances of political collaboration between Gen Musharraf and Ms Bhutto.
Attempts to pass a new bill failed in September in the face of angry opposition from the Islamists as well as some sections of Gen Musharraf's political allies.
Subdued
The version of the Women's Protection Bill put before legislators then caused such an outcry that parliament was prorogued.
Gen Musharraf has said women need to be better protected
But the MMA's top leader in parliament, Maulana Fazlur Rahman, was rather subdued in his opposition of the proposed legislation when it was tabled on Wednesday, media reports said.
A hardline MMA leader, Qazi Hussain Ahmed, did not attend the session at all.
Under the amended bill, rape cases will be tried in civil courts
Adultery, which has always been illegal, will still be tried by both civil and Sharia courts, depending on which system the complainant chooses.
Religious parties called the new legislation "a harbinger of lewdness and indecency in the country", and against the strictures of the Koran and Sharia law.
The government has said that some of the MMA's proposals were included in the bill. The MMA disputes this.
Islamist groups have vowed large scale protests after Pakistan's  amended laws to transfer rape cases from Sharia courts to .

Sharia courts in Pakistan, based on Islamic religious law, try rape cases under "''''" laws instituted in 1979. The laws say that a rape victim must herself face  charges unless she can produce four Muslim male witnesses to the rape. The maximum sentence for adultery is death by .

The laws are widely condemned by women's rights groups as an almost impossible burden of proof. Human rights groups have long campaigned for changes to the religious laws. On Wednesday, Parliament voted overwhelmingly in favor of the amendments.

A coalition of Islamic parties, the  (MMA), which forms the Parliamentary opposition, has opposed the changes, saying it encourages "free sex". The MMA says that its members will resign from national and provincial assemblies in protest.