In a hammer blow to the prime minister’s personal authority, 22 Conservative backbenchers voted against the Windsor Framework he negotiated with the EU, with around 50 more abstaining.
Former prime ministers Boris Johnson and Liz Truss were among the Tory rebels, as was ex-Tory leader Iain Duncan Smith and Jacob Rees-Mogg.
The DUP’s MPs also voted against the agreement, but it still passed by 515 votes to 29 after it was backed by Labour, the SNP and Lib Dems.
Under the Windsor Framework, which Sunak agreed with European Commission president Ursula von der Leyen last month, the current customs border in the Irish Sea would be all-but removed.
Sunak has also claimed that a “Stormont brake” would allow the government to veto any new EU laws from being imposed on Northern Ireland.
But the European Research Group of hardline Tory Brexiteers said the measure was “practically useless” and would still leave Northern Ireland subject to EU laws.
Boris Johnson said the government should instead pass the Northern Ireland Protocol Bill, which would allow ministers to unilaterally rip up parts of the existing deal – which he negotiated – between the UK and Brussels.
He said: “The proposed arrangements would mean either that Northern Ireland remained captured by the EU legal order – and was increasingly divergent from the rest of the UK – or they would mean that the whole of the UK was unable properly to diverge and take advantage of Brexit.
“That is not acceptable. I will be voting against the proposed arrangements today. Instead, the best course of action is to proceed with the Northern Ireland Protocol Bill, and make sure that we take back control.”
The deep splits within the Tory Party over Brexit were also on display during the 90-minute debate which preceded today’s vote.
Shadow Northern Ireland secretary Peter Kyle said: “We are acting in the national interest, they are riven with division.”
Lib Dem foreign affairs spokesperson Layla Moran MP said: “Another day and another Conservative party rebellion. We’ve all had enough of this chaos.
“Conservative MPs are like mutinous pirates who no longer care what their captain says. After today’s latest debacle, it is time they abandoned ship and made way for serious politicians.”