In order to permit prime minister's Brexit law advance, the law makers voted 326 to 29 in a vote post midnight.
These included limiting delegated powers, giving parliament the final vote on the EU withdrawal agreement and restoring the EU Charter of Fundamental Rights.
The bill basically seeks largely to copy and paste European Union law into British legislation to ensure the country has functioning laws and the same regulatory framework as the bloc at the moment of Brexit, something the government says provides certainty for companies.
These amendments are backed by normally loyal Tory MPs, such as John Penrose, Vicky Ford and Tom Tugendhat. Surely the brexit voters didn't believe that it would be them taking back control?
Lawmakers debated Prime Minister Theresa May's plan to repeal European Union laws and assimilate them into British law on Monday ahead of a vote that she was expected to win, but stronger opposition is likely in further votes over the next few weeks.
On Monday Nicola Sturgeon called for all parties to work together to safeguard Holyrood in the face of Brexit "threatening the underpinning principle" of devolution.
The government's bid to extract the United Kingdom from EU law in time for Brexit has passed its first Parliamentary test. MPs backed the EU Withdrawal Bill by 326 to 290 in a Monday late-night vote despite critics saying it represented a "power-grab" by ministers.
The Scottish Parliament has no power to veto Brexit.
Fine Gael MEP Mairead McGuinness, vice-president of the European Parliament, said some of the UK's 73 seats will be redistributed once it leaves the bloc and all outstanding legal issues are dealt with.
A prominent MP has said last night's rebellion on the EU Withdrawal Bill was expected, while describing the legislation as "dreadful".
"Ministers expressed a willingness to consider making procedural concessions to avoid defeat at the hands of a number of Conservative rebels, who signalled that they will join forces with opposition MPs to neuter what shadow Brexit secretary Keir Starmer called a "great power grab" by the executive".
"If you disagree with anything the Government does on Brexit, you are a Brexit betrayer", she said.
The matter divided Cumbria's MPs with three voting in support of the bill and three against.
"That's why I'm urging all MPs of all parts of the United Kingdom to come together in support of this crucial legislation so that we can leave the European Union safe in the knowledge that we are ready for day one of exit".