It will be debated by the House of Lords from the end of January.
The flagship EU (Withdrawal) Bill, if approved, will pass to the upper House of Lords, where it will undergo further scrutiny from the largely pro-EU chamber before being put to another vote.
Shadow Brexit secretary Sir Keir Starmer, speaking during the Bill's third reading in the Commons, said: "This Bill has never been fit for objective: it was not fit for goal when it started its life previous year and after 64 hours at committee and 10 hours at report it is still not fit for goal".
The vote on the bill's third reading followed two hours of voting on MPs' proposed amendments to the legislation, which the Government defeated.
Prime Minister Theresa May faced a setback last month when 11 of her own Conservative MPs voted with the main opposition Labour Party for an amendment to have a meaningful vote on the terms of Brexit.
The government breathed a sigh of relief tonight as MPs approved its European Union withdrawal bill, setting the scene for a showdown over the flagship Brexit legislation in the House of Lords.
Brexit Secretary David Davis said the government would present a number of amendments to the bill when it reaches the Lords
"I hope and believe that the other place [the Lords] will make an enormous number of changes to this bill", he said.
During the first of two days of Commons debate yesterday, Conservative MP and leader of the rebellion, Dominic Grieve, raised concerns over plans not to bring the European Union charter of fundamental rights into British law post-Brexit.
Justine Greening, who resigned as education secretary in a reshuffle earlier this month, warned that if Brexit did not work for young people, "it will not be sustainable" and they may seek to "improve or undo what we've done".
British MPs resumed discussions Tuesday on a landmark piece of legislation allowing Britain to leave the European Union, on the eve of a vote on the draft law.
European Council President Donald Tusk on Tuesday said the EU's "hearts were still open" if Britain chose to change its mind about leaving the bloc.More news: Lawmakers react to government shutdown; what's impacted in Hawaii