The prime minister was forced into concessions by the rebels, including giving MPs another vote on tiers before February 3, and offering drinks-only pubs £1,000 each to get through December.
Despite this, Johnson still faced a major backlash from his own MPs and only managed to win approval for the tiers system from a minority of MPs after Labour, the SNP and Liberal Democrats abstained.
The PM won the vote by 291 votes to 78, majority 213.
A breakdown of the vote showed a major rebellion from 55 Tory MPs, while 18 Labour MPs also voted against the measures.
The backlash against Johnson is well over the 40 or so needed to threaten his majority in future if all opposition parties join the rebels in voting against the government.
The vote will mean every area on the English mainland, apart from Cornwall, entering either tier 2 or tier 3 Covid restrictions from after midnight tonight, when England’s lockdown ends.
The regulations have been strengthened from the pre-lockdown version to stop pubs in tier 2 serving alcohol unless it is alongside a substantial meal, and to close hospitality entirely in tier 3.
The plans were condemned by senior Tory MPs from across the party.
Sir Graham Brady, who chairs the powerful 1922 committee of Tory backbenchers, said Johnson had failed to make the case for the restrictions despite publishing an economic and health analysis requested by rebels.
Conservative MP Sir Graham Brady says his Trafford constituents have been placed "unfairly" in tier 3
"In the absence" of explanation or a clear route to the lower tier, he says he "has no choice but to oppose" the Covid restrictions https://t.co/T8xDvBCMXd pic.twitter.com/hrxQcMNj76
— BBC Politics (@BBCPolitics) December 1, 2020
He said his Altrincham and Sale West constituency had been “unfairly” placed in tier 3, telling MPs: “I looked in vain at the document published late yesterday for any explanation or any route being set out as to how we would reach that lower tier.
“In the absence of that serious and compelling case, I have no choice but to oppose these measures.”
Damian Green, who chairs the One Nation caucus of centrist Tories, said the government’s failure to explain what constitutes a substantial meal was indicative of an approach that was unlikely to command public confidence.
“I put to the prime minister last week the thoughts of a constituent who said that if the government imposes stupid rules, people will stop obeying the sensible rules as well,” he said.
“This was sadly dismissed. Since then, the national debate has moved on to how big a scotch egg has to be to constitute a substantial meal. I rest my case.”
Mark Harper, who chairs the Covid Recovery Group of Tory rebels, told Johnson to start “start treating members of parliament properly” by setting out the full analysis of the impact of restrictions.
Former cabinet minister David Davis called for restrictions to be far more localised, which Johnson hinted could happen when the restrictions are reviewed for the first time in two weeks.
Conservative MP David Davis will not vote for Covid tier measures in England
"We must follow the example of Germany, South Korea and others, by having restrictions imposed on a much smaller area," he says https://t.co/T8xDvBCMXd pic.twitter.com/h56E1KfQPS
— BBC Politics (@BBCPolitics) December 1, 2020
“In this country, we do not give up our freedoms lightly,” he said.
“What we need today is a policy of maximum protection for minimum damage, this policy is not it and I hope the next iteration in February does a much better job.”
Ex-attorney general Jeremy Wright said he was voting against the government “for the first time in 10 years”, and called for restrictions to be applied at borough and district level rather than county-wide.
Tobias Ellwood, Conservative chairman of the Commons defence committee, said: “No.10 is overwhelmed, the bandwidth cannot cope with everything that’s going on.
“You’ve got Covid-19, you’ve got the economic intervention, you’ve got Brexit, the integrated (defence) review, preparing for COP26 and then you’ve got the G7 presidency as well.
“It’s the same people who are not, I’m afraid, these are friends of mine, but they are not trained in crisis management and strategic planning or indeed in emergency response.”
Some Labour MPs also rebelled against Keir Starmer’s order to abstain by choosing to vote against the restrictions.
Labour MP Graham Stringer said the restrictions themselves harmed his constituents’ health.
“Remember, poverty kills,” he said.
“It is not just cancer and Covid that kills, poverty kills, people commit suicide.
“Children who have had their education withdrawn – suicide rates amongst children are up by 40% – so there is huge damage done across the board.”
Following the vote, a government spokesperson said: “We welcome tonight’s vote which endorses our winter plan, brings an end to the national restrictions and returns England to a tiered system.
“This will help to safeguard the gains made during the past month and keep the virus under control.
“We will continue to work with MPs who have expressed concerns in recent days.”
This article originally appeared on HuffPost UK and has been updated.