But his threat did not scare 21 Tories who on Tuesday night defied him to back plans for backbenchers to take control of the Commons order paper on Wednesday.
The government lost the vote 328 to 301.
Sir Nicholas Soames, the grandson of Johnson’s hero and World War Two PM Winston Churchill, was among the rebels.
Here is the full list of Tory rebels:
Guto Bebb
Richard Benyon
Steve Brine
Alistair Burt
Greg Clark
Ken Clarke
David Gauke
Justine Greening
Dominic Grieve
Sam Gyimah
Philip Hammond
Stephen Hammond.
Richard Harrington
Margot James
Oliver Letwin
Anne Milton
Caroline Noakes
Antoinette Sandbach
Nicholas Soames
Rory Stewart
Ed Vaizey
It comes after Johnson, who has pledged to deliver Brexit on October 31 “do or die”, said he would shutdown parliament for five weeks, sparking nationwide protests.
Independent MP Nick Boles, who left the Conservative party in April, during the debate called for rebel Tories to cross the floor and join him on the opposition benches.
He said he was able to “hold his head high” after leaving the party.
“At the moment, I am the only independent progressive Conservative in parliament,” he said.
“To those brave souls on the Conservative benches who face expulsion from the party for voting for the motion today, I say this: your country needs you.
“Do what you know to be right.
“Join me on these benches and, together, let us build a new force in British politics and a true home in parliament for those who believe in one nation.”
The same MPs look set to give the government another bloody nose tomorrow when MPs try to push through a new law to force Johnson to delay Brexit in the face of no-deal.