Labour's Hilary Benn says: "The size of the majority today - 41 votes - sends a very clear message to the next prime minister that Parliament is resolute on this question."
"If you think you can tell us to go away until 31 October, Parliament will not allow that to happen," he says.
As MPs have - through the Benn-Burt amendment - changed the bill, it will now go back to the House of Lords for approval.
This is part of a process known as "ping pong", whereby a bill goes between the Commons and Lords until both Houses agree on the exact wording.
Who were the Conservative rebels?
Seventeen Conservative MPs rebelled against the government by voting for the Benn-Burt amendment:
Guto Bebb
Steve Brine
Alistair Burt
Jonathan Djanogly
Justine Greening
Dominic Grieve
Sam Gyimah
Richard Harrington
Margot James
Philip Lee
Jeremy Lefroy
Oliver Letwin
Paul Masterton
Sarah Newton
Antoinette Sandbach
Keith Simpson
Ed Vaizey
'Parliament can't be bypassed'
BBC News Channel
Conservative MP Alistair Burt - who proposed today's amendment - says: "Parliament can't be bypassed."
"The message from MPs today is that trying to get something down without Parliament being there won't work," he adds.
Prorogation 'would put Queen in a difficult situation'
BBC News Channel
Constitutional expert Professor Meg Russell says today's votes represent "quite a heavy defeat" for the government, putting "practical obstacles" in the way of ministers seeking to close down - or prorogue - Parliament.
"On one level prorogation is absolutely normal - It is not a dirty word," she says.
"But what is unusual is the idea of proroguing Parliament for a political reason - that is a very, very problematic idea.
"Using prorogation as a political tool risks bringing the monarch into politics, as she needs to give her consent to close down Parliament.
"That would put the Queen in a very difficult situation."
What do today's government defeats mean?
MPs have voted to make it more difficult for a new prime minister to use the mechanism of proroguing Parliament to force through a no-deal Brexit.
They backed the "Burt-Benn" amendment by 315 to 274 votes. This would require a minister to make statements to the Commons, even if Parliament had been suspended.
In a second government defeat, by 315 to 273 votes, they endorsed last night's Lords amendment, to ensure Parliament sits for a fortnightly debate on government updates on the restoration of power-sharing in Northern Ireland.
These defeats will make it harder - but not impossible - for Boris Johnson to prorogue Parliament if he becomes prime minister. And even if he does manage to suspend it, these legislative devices will mean that the Commons can still meet, debate and hold votes during that prorogation period.
BreakingSecond government defeat: MPs endorse fortnightly debates on Northern Ireland power sharing
MPs vote to approve last night's Lords amendment by 315 votes to 273.
MPs vote on original Lords amendment
House of Commons
Parliament
MPs are now voting on the motion that the House of Commons disagrees with the original Lords amendment as amended by Hilary Benn and Alistair Burt.
This is an attempt by the government to get rid of the amendment blocking a shut down of Parliament.
Government opposing amendments to block no-deal Brexit
House of Commons
Parliament
The government warned that Parliament is "weaponising" the NI bill, by attempting to amend it with UK-wide Brexit issues to do with Brexit:
Quote Message: This change will set a constitutional precedent that could last for centuries, whether we intend it to or not. We should not do it like this, not in this bill and not in this way. from John Penrose Northern Ireland Minister
This change will set a constitutional precedent that could last for centuries, whether we intend it to or not. We should not do it like this, not in this bill and not in this way.
The debate concludes and MPs begin voting on Hilary Benn and Alistair Burt's amendment.
This amendment explicitly blocks prorogation - the suspension of Parliament - between 9 October and 18 December.
Minister wraps up debate on Northern Ireland Bill
House of Commons
Parliament
Shadow Northern Ireland secretary Tony Lloyd confirms Labour will be supporting Hilary Benn's amendment.
Northern Ireland Minister John Penrose urges MPs to reject the amendment arguing it is "trying to prevent the democratic referendum decision from ever happening at all".
MPs are shouting at the minister as he finishes his words.
Abortion amendment 'extreme'
House of Commons
Parliament
DUP MP Ian Paisley says the abortion amendment would create "extreme laws", allowing "the termination of life at the point of birth".
"How cheap do they hold life," he asks. "The appear to hold it very low indeed."
Live Reporting
Kate Whannel, Thomas Mason and Richard Morris
All times stated are UK
'Half a dozen' cabinet members didn't vote on Benn-Burt amendment
Labour MP tweets...
Benn: Parliament intends to be here
BBC Politics tweets...
'Parliament is resolute on this question'
BBC News Channel
Labour's Hilary Benn says: "The size of the majority today - 41 votes - sends a very clear message to the next prime minister that Parliament is resolute on this question."
"If you think you can tell us to go away until 31 October, Parliament will not allow that to happen," he says.
MPs have not yet blocked a no-deal Brexit
BBC political editor tweets...
Bill in 'ping pong' stage
BBC political editor tweets...
As MPs have - through the Benn-Burt amendment - changed the bill, it will now go back to the House of Lords for approval.
This is part of a process known as "ping pong", whereby a bill goes between the Commons and Lords until both Houses agree on the exact wording.
Who were the Conservative rebels?
Seventeen Conservative MPs rebelled against the government by voting for the Benn-Burt amendment:
'Parliament can't be bypassed'
BBC News Channel
Conservative MP Alistair Burt - who proposed today's amendment - says: "Parliament can't be bypassed."
"The message from MPs today is that trying to get something down without Parliament being there won't work," he adds.
Prorogation 'would put Queen in a difficult situation'
BBC News Channel
Constitutional expert Professor Meg Russell says today's votes represent "quite a heavy defeat" for the government, putting "practical obstacles" in the way of ministers seeking to close down - or prorogue - Parliament.
"On one level prorogation is absolutely normal - It is not a dirty word," she says.
"But what is unusual is the idea of proroguing Parliament for a political reason - that is a very, very problematic idea.
"Using prorogation as a political tool risks bringing the monarch into politics, as she needs to give her consent to close down Parliament.
"That would put the Queen in a very difficult situation."
What do today's government defeats mean?
MPs have voted to make it more difficult for a new prime minister to use the mechanism of proroguing Parliament to force through a no-deal Brexit.
They backed the "Burt-Benn" amendment by 315 to 274 votes. This would require a minister to make statements to the Commons, even if Parliament had been suspended.
In a second government defeat, by 315 to 273 votes, they endorsed last night's Lords amendment, to ensure Parliament sits for a fortnightly debate on government updates on the restoration of power-sharing in Northern Ireland.
These defeats will make it harder - but not impossible - for Boris Johnson to prorogue Parliament if he becomes prime minister. And even if he does manage to suspend it, these legislative devices will mean that the Commons can still meet, debate and hold votes during that prorogation period.
BreakingSecond government defeat: MPs endorse fortnightly debates on Northern Ireland power sharing
MPs vote to approve last night's Lords amendment by 315 votes to 273.
MPs vote on original Lords amendment
House of Commons
Parliament
MPs are now voting on the motion that the House of Commons disagrees with the original Lords amendment as amended by Hilary Benn and Alistair Burt.
This is an attempt by the government to get rid of the amendment blocking a shut down of Parliament.
MPs make it 'harder' to shut down Parliament
BBC political editor tweets...
BreakingMPs approve Benn/ Burt amendment
House of Commons
Parliament
MPs have voted to approve the amendment 315 votes to 274.
Minister votes against government
BBC Newsnight political editor tweets...
Government defeat?
BBC Newsnight political editor tweets...
Government opposing amendments to block no-deal Brexit
House of Commons
Parliament
The government warned that Parliament is "weaponising" the NI bill, by attempting to amend it with UK-wide Brexit issues to do with Brexit:
Heckling from MPs as minister winds up
PA political reporter tweets
MPs begin voting
House of Commons
Parliament
The debate concludes and MPs begin voting on Hilary Benn and Alistair Burt's amendment.
This amendment explicitly blocks prorogation - the suspension of Parliament - between 9 October and 18 December.
Minister wraps up debate on Northern Ireland Bill
House of Commons
Parliament
Shadow Northern Ireland secretary Tony Lloyd confirms Labour will be supporting Hilary Benn's amendment.
Northern Ireland Minister John Penrose urges MPs to reject the amendment arguing it is "trying to prevent the democratic referendum decision from ever happening at all".
MPs are shouting at the minister as he finishes his words.
Abortion amendment 'extreme'
House of Commons
Parliament
DUP MP Ian Paisley says the abortion amendment would create "extreme laws", allowing "the termination of life at the point of birth".
"How cheap do they hold life," he asks. "The appear to hold it very low indeed."