The government won by a narrow margin as MPs voted 319 to 303 against the amendment that was tabled by leading pro-EU Conservative Dominic Grieve.
Theresa May's flagship Brexit bill has cleared its final parliamentary hurdle after she avoided a backbench rebellion with an eleventh hour concession to pro-EU Tories.
Six Tory MPs - Ken Clarke, Anna Soubry, Sarah Wollaston, Heidi Allen, Antoinette Sandbach and Phillip Lee - rebelled while four Labour MPs backed the government and six other Labour MPs abstained, as did Kelvin Hopkins, who sits as an independent after having the whip withdrawn.
It will mean a new cliffhanger when MPs vote on Wednesday to decide how much of a say the British Parliament should have on a Brexit deal.
"Over the next few weeks we will publish more details of our proposed future relationship with the European Union in a White Paper, and will bring the Trade and Customs Bills back to the House of Commons", said May.
"The government can not be forced by Parliament to negotiate something that the government does not want to do", the global trade secretary stated before the vote.
It would also effectively take "no deal" off the table, .
Bradford West's Naz Shah, who has been ill, was pushed in to vote in a wheelchair with a sick bucket on her lap, in scenes which fellow Labour MP Catherine McKinnell said showed an "utter lack of humanity and compassion" from the Government.More news: LeBron prefers staying with Cleveland
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Potential Tory rebels were bristling at Theresa May's plan to offer only a symbolic vote on an unamendable "neutral motion" which would simply note that no agreement has been reached with Brussels.
Downing Street left no doubt ministers were confident of drafting a motion which Mr Bercow will deem to be unamendable.
Mr Grieve said that the Brexit Secretary's statement amounted to an "obvious acknowledgement of the sovereignty of this place over the executive in black and white language".
Meanwhile pregnant Liberal Democrat deputy leader Jo Swinson and Labour MP Laura Pidcock turned out to oppose the PM's plans despite being close to their due dates.
But the government tried to ease Grieve's and others' concerns in a statement that said it was up to the parliamentary speaker to grant lawmakers greater influence over the future action of ministers if there was no deal.
The Prime Minister staved off a Tory rebellion on the move last week but faces a bruising battle in the latest round of voting amid claims she failed to implement a compromise that opponents believed they were promised.
Leading Brexiteer Jacob Rees-Mogg told Sky News Mrs May would now attend a summit of European Union leaders next week "with full strength, with the ability to say the legislation to leave the European Union, under EU law and United Kingdom law, is now fully in place".