Philip Hammond joined other Tory rebels in a successful attempt to block Boris Johnson from forcing a no-deal Brexit by suspending parliament.
Johnson, the frontrunner to succeed Theresa May as prime minister next week, has not ruled out proroguing parliament ahead of the October 31 Brexit deadline.
If he did so MPs would not be able to change the law to prevent a no-deal exit.
But on Thursday the Commons voted 315 to 274 in favour of a cross-party amendment to the Northern Ireland (Executive Formation) Bill to stop prorogation - a majority of 41.
May had ordered Tory MPs to vote against the move. But the chancellor, International Development Secretary Rory Stewart, Business Secretary Greg Clark and Justice Secretary David Gauke defied the whip and abstained.
In normal circumstances their decision would mean they would have to resign from the cabinet or be sacked by the prime minister.
But Downing Street said while May was “disappointed” in their actions it was for her successor to “take this into account when forming their government”.
Hammond, who has warned a no-deal could cost the UK economy £90bn, is expected to be consigned to the backbenchers if Johnson becomes prime minister.
Margot James, the digital minister, resigned from the government after voting in favour of the amendment.
The rebel ministers were joined by 17 other Tory MPs who went even further and voted in favour of the change.
Jeremy Hunt, the foreign secretary and Johnson’s rival for No.10, did not vote and later admitted he thought he had been granted permission.
Jonathan Djanogly, one of the backbench Tory rebels, tweeted: “Prorogation for Brexit purposes would have been damaging to our constitution and the Conservative Party and have led to civil insurrection and violence.”
Johnson, who has said the UK is leaving the EU on October 31 “do or die” voted, against the move to block prorogation.
Labour, the Lib Dems and the SNP all supported the move to prevent Johnson suspending the Commons.
Keir Starmer, Labour’s shadow Brexit secretary, said: “For Boris Johnson to try to shut down parliament to force through a destructive no-deal Brexit would be a constitutional outrage. Now it would also be unlawful. A huge victory.”
Justine Greening, a former Conservative cabinet minister told MPs today: “You don’t win a debate by closing down the main chamber in which this country’s people’s views are aired, and you don’t unite a country by muzzling the representatives of the people around those communities who have been democratically elected to come here and represent them.”
While Labour former minister Angela Eagle said Johnson appeared to think he could “behave like a Stuart king” by closing parliament.
“It did not end well in the civil war century and I warn the (next) prime minister it will not end well if he tries to do the same thing in the 21st century.”