Despite the opposition of 99 Conservatives, the motion was approved by 243 votes mainly to Labour backing.
From Wednesday, many large establishments, including nightclubs, require NHS Covid passes showing a recent negative test or full vaccination.
MPs also backed making face masks mandatory indoors.
Sir Geoffrey Clifton-Browne, a Tory dissident, said the size of the mutiny over passes implied a leadership challenge to Mr Johnson next year.
A rebellious Tory MP, Sir Charles Walker, told the BBC the rebellious Tory MPs were "crying of anguish" over the specific policy, which they saw as an affront on personal freedoms that would not stop Covid's expansion.
The Night Time Industries Association, which represents nightclubs, expressed fear that this would "jeopardise the future of enterprises in 2022" and demanded "immediate extra" government funding.
MPs voted for:
Vaccinate all NHS personnel in England
2-From Wednesdays, adults in England must provide proof of complete vaccination or a recent negative lateral flow test to attend major places like nightclubs.
In lieu of isolation, fully vaccinated people in touch with Covid patients undergo daily lateral flow checks.
4-Keep making face masks mandatory in more places.
Self-isolation was replaced by daily lateral flow testing for fully vaccinated people who come into touch with Covid cases, including Omicron.
Before the voting, the PM urged his MPs to back the government's Plan B proposals.
"We just cannot rely on the assumption Omicron may be moderate," he told Tory backbenchers.
According to Mr Johnson, even if Omicron symptoms were not as severe as the Delta variety, the levels of transmission would cause "disastrous" numbers of hospitalizations.
Backbenchers attacked the Covid pass idea, stating it would promote fear and do nothing to stem Omicron's spread.
To "criminalise the people of England for breaking regulations that many, it seems, cannot follow," warned South Dorset MP Richard Drax.
"A society where we ask for papers and rob individuals of their rights," remarked former minister Tim Loughton.
38 Tory MPs - and three DUP members - defied the government over the face mask scheme.
There was also a 63-MP Conservative revolt over mandatory vaccines for NHS workers.
Acting quickly would "help us have a safer Christmas and protect our NHS from being absolutely overloaded," said Labour's shadow health secretary Andrew Gwynne
"In a crisis, Labour would always put people and the nation's health above party politics," he continued.
Ex-shadow home secretary Diane Abbott and ex-Labour leader Jeremy Corbyn voted against Covid.