The prime minister's timetable was voted down by a majority of 14 in a dramatic late vote, with 308 MPs in favour and 322 against.
Moments earlier, Mr Johnson's Brexit deal bill cleared its first Commons hurdle with the support of a clutch of Labour MPs from Leave-voting constituencies.
However his plan to railroad the legislation through parliament before the Halloween deadline were emphatically rejected by MPs, who were not prepared to accept the tight timetable.
Mr Johnson's hopes were thwarted by his DUP allies, who voted against the programme motion out of anger at his Brexit blueprint. Nine of the 21 expelled Tories also opposed the plan, including ex-cabinet ministers Philip Hammond and David Gauke.
Speaking immediately afterwards, Mr Johnson said government will "pause" the bill until the EU reaches a decision on whether to offer the UK a Brexit extension.
He told MPs: "I will speak to EU member states about their intentions," adding: "Until they have reached a decision we will pause this legislation."
Mr Johnson added: "Our policy remains that we should not delay, that we should leave the EU on 31 October and that is what I will say to the EU and I will report back to the House.
"And one way or another we will leave the EU with this deal, to which this House has just given its assent."
Jeremy Corbyn offered to work with Mr Johnson to set a "reasonable" timetable for the scrutiny of the bill.
The Labour leader told MPs: "The prime minister is the author of his own misfortune. So I make this offer to him tonight.
"Work with us, all of us to agree a reasonable timetable, and I suspect this House will vote to debate, scrutinise and, I hope, commend the detail of this Bill."
But Jacob Rees-Mogg, the Commons leader, revealed the government would slam the brakes on the bill - and bring back the Queen's Speech debate instead, which had been put on ice.
Downing Street said Mr Johnson continues to believe the UK should leave the EU on 31 October and that an extension beyond this month would be "corrosive".
The prime minister's official spokesman said: "Where we are now as a result of the actions of parliament is that the EU will have to consider the request from parliament that was conveyed to it at the weekend."
The dramatic defeat on the timetable came after Mr Johnson won a 30-strong majority for his Brexit deal at the bill's second reading.
Some 19 Labour MPs defied Mr Corbyn to support the prime minister's deal, along with 18 expelled Tories, including Philip Hammond and Amber Rudd.