May's fragile government will be trying to defeat a rebellion by pro-EU lawmakers and reverse changes to its key piece of Brexit legislation as the matter comes before the House of Commons.
The result left Prime Minister Theresa May to fight another day as she tries to take Britain out of the bloc while retaining support from pro-EU and pro-Brexit wings of her Conservative Party.
Earlier May suffered a setback when junior justice minister Phillip Lee, who has always been critical of Brexit strategy, resigned and said he would vote against the government.
Hours before the debate began, a justice minister resigned in protest at what he called its "wish to limit" the role of parliament in shaping Brexit.
The new amendment, proposed by Conservative MP Dominic Grieve, will now be considered when the bill returns to the House of Lords, with government whips indicating to the rebels that they will accept the bulk of the amendment.
Earlier this year, Lee had called on the government to release its economic impact assessments of Brexit and suggested the government change tack in talks with the European Union, underlining the deep rifts in his party over the best way to manage Britain's exit.
In what is likely to be a highly-charged appearance before the backbench 1922 Committee on Monday, the Prime Minister is expected to say that the way MPs vote will send a message.
Opening the debate, Brexit Secretary David Davis insisted the government would abide by three principles to defend the will of the British people.
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Theresa May has averted an embarrassing defeat over the government's EU Withdrawal Bill by giving MPs a say on the next steps for Brexit if she fails to secure a withdrawal agreement by the end of November.
The Government has won this key vote, but not without having to make some significant concessions.
The victory - by 324 votes to 298 - only came after public haggling between ministers and would-be rebels and a meeting between Mrs May and more than a dozen Tory MPs.
May's divided cabinet has yet to settle on what sort of customs deal Britain should have with the European Union - an issue of crucial importance to businesses with cross-border supply chains, and the land border between European Union member state Ireland and the British province of Northern Ireland.
His competing amendment could force ministers to hand over control of its Brexit strategy to parliament if there is no deal by mid-February. May's preferred approach is temporarily keeping the U.K.in some form of temporary customs union with the E.U., but this is unacceptable to hardline Brexiteers in her party.
"The Brexit secretary has set out three tests that any new amendment has to meet - not undermining the negotiations, not changing the constitutional role of parliament and government in negotiating global treaties, and respecting the referendum result".
Matthew Pennycook, one of the opposition Labour Party's Brexit policy team, urged lawmakers to vote to hand parliament more powers.