It would force Mr Johnson to seek a three-month extension to the 31 October deadline unless parliament had either approved a deal or consented by 19 October or to leave without one.
All MPs opposed to a no-deal Brexit "should use the prorogation period to nail down an agreement on a caretaker government, headed by a more trustworthy and less divisive figure than Mr Corbyn, and on strategies for the following weeks and for an election".
Despite the vote, Johnson reiterated that he aims to meet the deadline, with or without a deal.
The Prime Minister said it was MPs' last chance to give the public an opportunity to vote on the various parties' Brexit strategies before the United Kingdom is due to leave the European Union on 31 October.
Labour said all opposition leader who met with Jeremy Corbyn's on Monday had "agreed to work together to hold the Government to account in Parliament".
Speaking in Ireland alongside Irish Prime Minister Leo Varadkar, Johnson said he was bringing ideas on ways to resolve the Irish border backstop but that a breakthrough was unlikely on Monday.
He called on Mr Johnson to reflect on his decision to suspend parliament.
The UK prime minister said there were three questions that must be answered: "Can we ensure that we have unchecked movement at the border?"
"In the absence of agreed alternative arrangements, no backstop is no deal for us", Varadkar, standing beside Johnson outside the Irish government, told reporters.
The law requires the government to seek a three-month delay from withdrawing from the EU.
MPs pack the Commons
Mr Johnson said: "It's plain from the turbulent reaction of the benches opposite that they simply want another delay and I will not have that".
Mr Johnson's fellow Tory MPs were never that keen on the former London mayor and only chose him because they saw him as the one figure they could rely on to see off the challenge from Nigel Farage's Brexit Party, win an election and save their seats.
"So, we have a no-deal Brexit, we have a no-debate Brexit, we have a no-democracy Brexit at the moment, and I think he is trying to hide the information from the country".
Commons Speaker John Bercow expressed his displeasure at Parliament's suspension, saying "this is not a standard or normal prorogation".
It was a final show of defiance in a stormy parliamentary session in which Johnson also lost a separate vote, calling on the government to publish confidential papers about the potential impact of a no-deal Brexit.
He said: "If there is a no deal, it would cause severe disruption for British and Irish people alike".
Treasury minister Simon Clarke has said the government will not ask the European Union for a Brexit extension, despite a law being passed that may require it to do so.
"We are open to alternatives but they must be realistic ones - legally workable - and we have not received such proposals to date".
"I think there are internal documents available to ministers that tell them of the risks that they can not guarantee medical supplies or food supplies, and I think they are avoiding debate on this".
Mr Johnson said opposition parties had decided they "know better" than the public.
Parliament's suspension ended a day of blows to the embattled Johnson.
Mr Johnson's political position in Britain has been weakened over the past week, with the loss of his Conservative Party's working majority in Parliament and the departure of some key party figures who sided with the opposition in key votes.