Tories had warned the economy of Manchester would be hit if opposition parties "scupper" their attempts to go ahead with their annual conference in the city next week.
But a motion asking for the Commons to be in recess on Monday, Tuesday and Wednesday next week was defeated by 306 votes to 289 - a majority 17 - earlier today.
Boris Johnson was said to be "disappointed" by the decision.
A source said: "If somebody needs to do PMQs, somebody will do PMQs."
The convention of allowing party conference to go ahead in recess had stood for 80 years, the source said, adding: "That this zombie Parliament has decided otherwise reflects much more on this Parliament than anyone else."
As First Secretary of State, Dominic Raab would normally be expected to stand in for the Prime Minister at the session.
The problem has arisen because Mr Johnson's plan to suspend Parliament was derailed by the Supreme Court, which ruled it was unlawful.
That meant the Commons and Lords will now be sitting on Monday, Tuesday and Wednesday.
The conference may have to be "scaled back" in places if MPs have to remain at Westminster, the senior Tory source acknowledged.
With the four-day event which starts on Sunday estimated to be worth more than £30 million to Manchester, the source said local businesses will suffer if it is curtailed.
A Number 10 source said: "If they do not allow Conservative Party conference to go ahead with a recess at the same time, it will be incredibly damaging for the economy of Manchester."
After the Government lost the vote, Commons Leader Jacob Rees-Mogg announced non-controversial business for when the House sits on Monday and Tuesday next week.
He added the Domestic Abuse Bill, which has cross-party support, will be debated on Wednesday.
"As the Prime Minister has made clear, the Conservative Party conference will go ahead as planned."
Speaking in the Commons, SNP MP Patrick Grady (Glasgow North) said: "My heart does bleed for the poor Conservative ministers and backbenchers who will have to come to the House now during their conference."
Mr Grady said the SNP conferences do not get a recess, despite the party's status as the third largest in the Commons.
The division list for the vote showed several former Tory ministers, now sitting as Independent MPs, opposed the recess motion.
They included Amber Rudd, Ken Clarke, David Gauke, Justine Greening and Dominic Grieve.
The Independent MPs to support the recess motion included former Tory ministers Greg Clark, Caroline Nokes and Steve Brine.