The Prime Minister was under pressure from hardliners to pull the flagship bill over fears it is too soft.
But he pushed ahead after a 24-hour intensive charm offensive won over enough wavering MPs to clear its first parliamentary hurdle with a comfortable majority of 44.
Mr Sunak said: “The British people should decide who gets to come to this country – not criminal gangs or foreign courts. That’s what this Bill delivers.”
“We will now work to make it law so that we can get flights going to Rwanda and stop the boats.”
Just minutes before voting began, the “five families” of right-wing factions with concerns about the legislation announced they would abstain instead of vote against the bill.
But its leaders warned they will try to torpedo the legislation in its final stages unless significant changes are made.
Mark Francois, chairman of the European Research Group, said if the bill remains unamended “we reserve the right to vote against it at third reading”.
Centrist MPs, however, have indicated they will oppose the plan if they believe it has been toughened up too much.
It leaves the Prime Minister with around a month to find a way to keep the legislation alive.
Mr Sunak hopes the Safety of Rwanda Bill will revive his stalled deportation plan by blocking legal challenges made on the claim that Rwanda is unsafe.
It would allow ministers to disapply the Human Rights Act but does not go as far as overriding the European Convention on Human Rights.
Mr Sunak held an hour-long breakfast summit over bacon rolls with potential rebels from the New Conservatives group, including deputy Tory chairman Lee Anderson, Miriam Cates and Danny Kruger.
Mr Kruger later told the Commons he could not support the bill as it was “unsatisfactory” and he called for legislation that “respects parliamentary sovereignty”.
The vote was feared to be on such a knife-edge that MPs who had been given permission to be away from parliament were ordered back to Westminster.
They included Climate Minister Graham Stuart, who was forced to return from the COP28 summit in Dubai to vote before returning to the talks in a 6,824 mile round trip.
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No Tory MPs voted against the bill but nearly 40 did not take part in the vote.
MPs clashed in the Commons over six hours of stormy debate about the legislation.
Tory former immigration minister Robert Jenrick, who quit in protest at the bill, accused the Government of “sophistry” in the claims being made about the powers it will introduce.
He said ministers must have the “full power of Parliament” to ignore injunctions from the European Court of Human Rights but warned the legislation will not make that happen.
Mr Jenrick suggested the measures it contains allowing the UK to ignore interim injunctions from the European Court of Human Rights is deceptive.
He said it was “inevitable” the Strasbourg court would impose more restrictions on deportations.
“The provision in the Bill is sophistry,” Mr Jenrick told the Commons.
Conservative former cabinet minister David Jones, deputy chairman of the European Research Group, said there were “numerous deficiencies” in the bill that would render it “inoperable and ineffective”.
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He added: “The last thing we want to do as a House is to expend a lot of time and a lot of agony over putting in place a Bill that doesn’t result in the flights to Rwanda and the deterrence that we need to illegal migrants.”
But Conservative former attorney general Sir Geoffrey Cox advised colleagues the bill would “collapse” if they removed the right of individuals to appeal in all circumstances.
He said: “If we eliminate it entirely, not only would this Bill collapse because it will be interminably impeded in the House of Lords, it will probably lead to the Rwandan government withdrawing and it’s conceivable the courts themselves may entertain for the first time a complex challenge of the right of this Parliament to do away with fundamental constitutional principles, such as access to a court.”
Centrists Sir Bob Neill, chairman of the Commons’ justice committee, backed the bill but warned that he would withdraw his support in the future if changes from the Tory right were accepted.
He said: “After a good deal of hesitation I shall support this bill tonight, but it is a hesitation that has been real, because for me it goes as close to the wind as one can constitutionally do.”
He added: “If it were to change and any of the safeguards that have been left in to be removed, then my support would go, because some people would then have pushed it over the line into the unacceptable and, in my judgment, the unconservative, and then I would not support it.”
Senior Tory Sir Edward Leigh warned colleagues they must pull together instead of operating as factions.
He said: “The Conservative Party, I hear of all these different groups. You know, a house divided is a house that is going to be destroyed. We have to work together. There is no other solution.”
A Tory rebel source said: “This bill has been allowed to live another day. But without amendments it will be killed next month. It’s now up to the government to decide what it wants to do.”
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