A majority of 41 approved an amendment that blocks suspension between 9 October and 18 December unless a Northern Ireland executive is formed.
Four cabinet ministers, including Philip Hammond, abstained and 17 Tory MPs rebelled, including minister Margot James, who has resigned.
Leadership contender Boris Johnson has not ruled out suspending Parliament.
His rival Jeremy Hunt has ruled out this move.
Ms James told the BBC attempting to suspend Parliament was “too extreme” adding: “I thought the time was right today to join people who are trying to do something about it.”
The four cabinet ministers who abstained are International Development Secretary Rory Stewart, Business Secretary Greg Clark and Justice Secretary David Gauke, as well as Chancellor Mr Hammond.
Mr Clark defended his decision to abstain arguing: “I couldn’t support the idea that we would allow the doors of Parliament to be locked against MPs at this crucially important time – that would be a constitutional outrage.”
Mr Hammond tweeted: “It should not be controversial to believe that Parliament be allowed to sit, and have a say, during a key period in our country’s history.”
Image copyrightUK PARLIAMENTImage captionMargot James told the BBC “I felt it was time to put my marker down”
A Downing Street spokesman said the prime minister was “obviously disappointed that a number of ministers failed to vote in this afternoon’s division”.
“No doubt her successor will take this into account when forming their government,” the spokesman said.
Labour leader Jeremy Corbyn said the vote was “an important victory to prevent the Tories from suspending Parliament to force through a disastrous no deal”.
BBC political editor Laura Kuenssberg said the Commons had now made it harder for a new prime minister to suspend Parliament.
If the 31 October deadline is reached without Parliament backing an agreement between the UK government and the EU, the UK is scheduled to leave the EU without a deal.
MPs have consistently voted against a no-deal Brexit, but the prime minister could try to get around that by suspending Parliament – proroguing – in the run-up to the deadline, denying them an opportunity to block it.
The amendment to the Northern Ireland (Executive Formation) Bill was put forward by MPs including former minister Alistair Burt and Brexit committee chairman and Labour MP Hilary Benn.
It would mean that if Parliament is prorogued when the government publishes reports on the situation in Northern Ireland, MPs must be recalled to debate them.
Mr Burt told the BBC that Parliament had said “very clearly please don’t bypass us… Parliament must be sitting in the run up to 31 October”.
