The non-binding motion pressing the Government to maintain the increase was approved by 278 votes to zero, majority 278.
According to the division list, Tory MPs Peter Aldous, ex-work and pensions secretary Stephen Crabb, Robert Halfon, Jason McCartney, Anne Marie Morris and Matthew Offord rebelled to support the motion.
The standard Universal Credit allowance, which is claimed by more than 5.5 million households, was increased by £20 a week in April 2020 as part of Chancellor Rishi Sunak's early Covid economic response.
Although it was implemented as a temporary add on to help those unable to work or struggling due to the lockdown, opposition parties and charities say failing to extend will cause real hardship for hundreds of thousands of people.
Senior Tory Mr Crabb, rebelling for the first time against the party whip, said the weekly rise should be kept for a further 12 months in order to give people “certainty” over their finances.
Shadow work and pensions secretary Jonathan Reynolds said: “It is disappointing that the Conservative government refused to vote with Labour to provide families with certainty and secure our economy.
“They can still do the right thing and drop their plans to cut Universal Credit.
“Britain is facing the worst recession of any major economy because of the Government’s incompetence and indecision. Families cannot be made to pay the price.”
Labour leader Sir Keir Starmer tweeted that the Conservatives “didn’t even show up” after the vote.
Treasury minister Steve Barclay said the Government is “acutely aware” of the harm caused to finances by the Covid-19 pandemic.
“It’s clear that there is a heartfelt desire shared across all sides of the House to support constituents impacted by the economic consequences of Covid,” said Mr Barclay.
“As a government, we are acutely aware of the harm caused by the crisis to people’s finances including the most vulnerable in our society. At every stage of the pandemic, we have striven to support those who have found themselves at the sharp end.
“That’s why, as (Will Quince) earlier outlined, we introduced a wide-ranging package of welfare measures worth over £7 billion this year.
“As (Mr Quince) also pointed out, given the evolving nature of this pandemic, it is right that we wait until the budget to make future tax and welfare decisions.”
Downing Street insisted no decision has been made on whether to keep or scrap the increase, and said Chancellor Rishi Sunak will update the public on the Government’s plans “shortly”.
Mr Johnson repeatedly declined to state whether or not the increase will be extended when questioned during a visit to Oxfordshire.
“What we have said is we will put our arms around the whole of the country throughout the pandemic,” the Prime Minister told reporters.
“We have already done £280 billion worth of support and we will keep all measures under constant review.”
He added: “It’s the policy of the opposition to abolish Universal Credit altogether, which I don’t think is a sensible way forward.”
The Prime Minister was also facing pressure from the 65 Conservative MPs in the Northern Research Group (NRG), who said ending the increase would be “devastating”.
The Resolution Foundation warned that scrapping the £20-a-week uplift will lead to a particularly tough 2021 for low-income households, whose incomes could fall by 4 per cent.
The think tank estimated that the withdrawal of the benefit increase would drive up relative poverty from 21 per cent to 23 per cent by 2024-25, pushing a further 730,000 children into poverty.
Additional reporting by PA Media.