This signifies that 90 Labour MPs rebelled the whip in total, with 75 voting for the amendment and 15 voting against.
Dominic Grieve, the former Attorney General, took up the Lords' meaningful vote clause and ran with it in the Commons.
Theresa May'sBrexit truce risked being unravelled as Remainers indicated she faced a future rebellion if a compromise is not reached on the role of MPs in the divorce settlement.
Both Houses of Parliament must agree on the form of the EU Withdrawal Bill, and if the Lords insist on their amendment then the Commons will again be invited to reject it.
MPs voted by 324 to 298 to reject a House of Lords amendment to the EU Withdrawal Bill which would have given MPs the power to tell the Prime Minister to go back and renegotiate the Brexit deal.
"We are walking on a tightrope at the moment, we campaigned for remain but many of our MPs, including myself, now represent seats which voted heavily leave", John McDonnell, the party's economy spokesman and Corbyn's right-hand man said at an event in London on Wednesday. At one point, six Labour frontbenchers quit party posts in defiance over Corbyn's single-market policy.
It agreed to work towards a "customs arrangement" with the European Union in a compromise move, and gave a concession to rebels on a vote to give Parliament a "meaningful vote" on a Brexit deal.
"It could be the United Kingdom unintentionally crashing out of the European Union with no deal simply because time runs out".
Leading pro-EU Conservative Sarah Wollaston announced she would vote with the Government so long as a promised further amendment in the Lords "closely reflects" the Grieve proposals.
You only needed to look at the size of the amendment paper MPs had to consider to see how squeezed for time the debate was going to be.
This amendment had looked risky for the prime minister.
Speaking in Munich, he welcomed political settlements in the House of Commons but warned "this can't be Britain just negotiating with itself; the real negotiation has to happen between the British negotiating team and the European Union negotiation team". The government should be investing more in housing, the health service and education to relieve pressure on services, he said, not ending free movement of labor.
On Tuesday, parliament will also debate other amendments, including a challenge to the government's plan to put March 29, 2019, or "Brexit Day", into law and an attempt to toughen a commitment to ensure a frictionless border between Northern Ireland and the neighbouring Irish Republic, which will remain in the EU. This is where Conservative rebels like Nicky Morgan, Anna Soubry and Ken Clark are expected to make their biggest move on customs. However, the party is divided on the issue, with a total of 89 Labour MPs choosing to defy Corbyn. Davis has suggested he will resign several times since entering the job two years ago, and each time he failed to do so has strengthened May's position.
Elsewhere in a day of drama, the main opposition Labour party suffered a large rebellion by its MPs seeking to keep Britain in the EU's single market. It was a measure of the division in the party that out of 257 Labour MPs, 90 ignored that instruction and voted.
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