The Prime Minister said he would table a motion under the Fixed-term Parliaments Act on Tuesday night.
But Labour indicated that they would not support the move until chances of a no-deal Brexit were taken off the table.
Downing Street confirmed that the Tory rebels – including former chancellors Ken Clarke and Philip Hammond – would lose the Conservative whip as a result of their actions.
Withdrawing the whip means that an MP or Lord is effectively expelled from their party, but hangs onto their seat.
Johnson told the House of Commons after he was defeated in his first vote: “The consequences of this vote tonight means that Parliament is on the brink of wrecking any deal that we might be able to get in Brussels.
“It will hand control of the negotiations to the EU.”
He continued: “I don’t want an election but if MPs vote tomorrow to stop the negotiations and to compel another pointless delay of Brexit, potentially for years, then that will be the only way to resolve this.
“I can confirm that tonight we will are tabling a motion under the Fixed-term Parliament Act.”
Moments earlier MPs voted in favour of allowing a cross-party alliance to take control of the Commons agenda on Wednesday in a bid to block a no-deal Brexit on October 31 by 328 votes to 301, majority 27.
Analysis of the Commons division list showed 21 Tories rebelled to support the motion.
Former Cabinet ministers Hammond, Rory Stewart, Clarke, David Gauke and Greg Clark were among the Tories who rebelled in the key vote.
Sir Nicholas Soames – Winston Churchill’s grandson – also backed the rebel move.
A Downing Street spokesman said: “The Chief Whip is speaking with those Tory MPs who did not vote with the Government this evening. They will have the whip removed.”
Sir Nicholas told BBC Two’s Newsnight that he will not stand in the next election.
A source close to the rebels said: “Tonight’s decisive result is the first step in a process to avert an undemocratic and damaging no deal.
“No 10 have responded by removing the whip from two former chancellors, a former lord chancellor and Winston Churchill’s grandson. What has has happened to the Conservative Party?”
Labour leader Jeremy Corbyn told the Prime Minister: “He wants to table a motion for a general election, fine.
“Get the Bill through first in order to take no deal off the table.”
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