But the bill's passage through the House of Lords in the coming weeks could be far harder because the upper chamber is dominated by the pro-EU opposition.
Heralding the moment, Brexit Secretary David Davis said: "From the beginning our approach has been to work constructively with MPs from across the House wherever possible to improve the Bill".
He added: "This is a critical piece of legislation that aims to maximise certainty for individuals and businesses after our exit".
That was defeated by a whopping 322 votes to 99 - a 223 majority.
MPs spent more than 80 hours considering the Bill, including more than 500 amendments and new clauses.
He said Labour had "repeatedly" pointed out "six serious defects in the Bill", and said: "But we have been talking to a brick wall".
The bill is now set for debate by the House of Lords.More news: Reality Star Pleads Guilty to Tax Fraud
The bill is created to copy all European Union law which now affects the United Kingdom into national law, whereupon it can be subsequently amended or scrapped.
The UK Government says the measure is necessary to avoid disruption of the UK's internal market and insists that it continues to make "good progress" in discussions with the Scottish Government.
These powers - dubbed "Henry VIII powers" by critics - would give the government to scrap workers rights and environmental protections that have been guaranteed through European Union law.
Announcing Labour's opposition to the bill at third reading, shadow Brexit secretary Sir Keir Starmer branded it "not fit for purpose" as he repeated demands for MPs to have a meaningful vote on any divorce deal with the EU.
The Scottish and Welsh governments are also concerned that the bill will allow the Conservative government to seize control over policy areas that they believe ought to be devolved to Holyrood and Cardiff.
However, while Tory rebel Remainers may have sat on their hands tonight, it's clear that the battle is far from over for May in passing this bill. Many lords are opposed to Brexit.
"Ministers will have extraordinary powers to make laws under this Bill, so it is vital that each of the UK's legislatures have the opportunity to scrutinise effectively regulations made under these highly unusual ministerial powers".