They voted 272 votes to 246 - a majority of 26 - in favour of a new clause 49 being added to the Health and Care Bill.
Earlier Boris Johnson had faced an explosion of cross-party anger over his move to water down the cap on social care costs.
The proposals involved a cap of ￡86,000 on personal care. But a late amendment on the plan originally drawn up by Sir Andrew Dilnot means support payments from local councils won't go towards it.
People will therefore have to pay ￡86,000 of their own money before reaching the cap.
Sir Andrew, an economist, joined the outcry and condemned the revised plan as "a catastrophe".
Backbenchers also hit out at the revision following fears poorer pensioners will be forced to pay all their savings and sell their home for adult social care in England.
Christian Wakeford, a Tory MP from the so-called "Red Wall" former Labour heartlands in the north of England, said: "To change, to move the goalposts after we've already been introduced this, it's not something I'm comfortable with.
"Especially when one of the main messages for introducing this levy was, 'You won't need to sell your house for care,' to get to a point where unfortunately you might need to and (it's) arguably our least welloff in society, our least welloff voters - again, it's not something I'm particularly comfortable with."
Shadow Health Secretary Jonathan Ashworth said: "If you live in a ￡1million house, perhaps in the Home Counties, 90 percent of your assets will be protected if you need social care.
"But if you live in an ￡80,000 terrace house in Hartlepool, Barrow, Mansfield or Wigan, for example, you lose nearly everything.
"That is not fair, that is not levelling up, it is daylight robbery."
Mr Johnson claimed his blueprint for the reform of elderly care remained "incredibly generous". But he had been braced for a damaging Commons rebellion in the vote.
Former chief whip Mark Harper, leading the Tory revolt, warned the move "potentially disadvantages the less well-off and those of working age with life-long conditions." Health ministers had not "properly worked with the sector or MPs to explain their thinking or decisions," he claimed.
Defending the move, the Prime Minister said: "These are incredibly generous and they are much better than the existing system."
Speaking at the Confederation of British Industry conference in South Shields, he said his overhaul would prevent sufferers from conditions such as dementia facing "catastrophic" care costs.
"Under the existing system nobody gets any support if they have assets of ￡23,000 or more. Now you get support if you have ￡100,000 or less, so we are helping people.
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"It is, in fact, more generous than some of the original proposals because it helps people not just who are in residential care but also people who benefit from domiciliary care as well.We are finally tacking a problem that has bedevilled this country for decades, been very, very unfair on people who have got dementia or Alzheimer's and been forced to face catastrophic, ruinous costs for that care when somebody who has cancer or some other affliction does not."
During last night's Commons debate, Health Minister Edward Argar insisted the revised plan was "better" than the original plan proposed by the Dilnot report.
Former Tory health secretary Jeremy Hunt said: "What we will end up with after this will be a whole lot better for people on low incomes than what we had before.
"It is nothing like as progressive as we had hoped but it is a step forward."
But Tory backbencher John Baron said there was concern among Tory MPs "and worry that the less well-off will be hardest hit".
Labour claimed analysis showed the changes will mean the average home-owner in two-thirds of northern areas will have to pay more towards their care.
In the Midlands a third will be worse off, it said.
Downing Street defended the Government's plan as "necessary, fair and responsible".
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