The House of Commons voted by 291 votes to 78 – a Government majority of 213 – for the new restrictions on Tuesday evening.
The Black Country, Staffordshire and Birmingham will all now be under the highest alert level of Tier 3 until at least December 16, when the measures will be reviewed for the first time.
It means members of more than one household are banned from mixing with one another in any setting indoors as well as in private gardens and most outdoor venues.
Hospitality settings, such as bars, pubs, cafes and restaurants must close, although takeaways and deliveries are still allowed.
Ahead of the vote a number of Conservative MPs criticised the restrictions, saying the Government's arguments to impose them were inadequate.
Fifty-five Conservatives rebelled over the measures, with 53 voting against the Government and a further two acting as tellers for the noes.
But the measures passed with Labour ordering its MPs to abstain after leader Sir Keir Starmer warned the plans pose a “significant” health risk.
No Conservative MPs in the Black Country and Staffordshire rebelled, but Labour MP for Warley John Spellar voted against the measures after warning the restrictions would be disastrous for the country's hospitality industry.
He said: "We are crashing a very significant industry, which is a big part of our way of life with minimal impact on the coronavirus, but with a huge impact on the economy and on society.
"It is not justifiable or necessary and simply shows that Matt Hancock and Michael Gove haven't got a clue."
A Government spokesman welcomed the backing from the Commons to “help to safeguard the gains made during the past month and keep the virus under control”.
But he said that ministers will “continue to work with MPs who have expressed concerns in recent days”.
The Prime Minister announced a one-off payment of £1,000 for pubs forced to remain closed under the restrictions in an attempt to reduce the scale of the revolt, though the move was branded “derisory” by the trade.
Mr Johnson acknowledged concerns of a perceived “injustice” in the allocation of tiers but reassured MPs that the Government would look at a more focused approach in the future.
The House of Lords was expected to approve the plans later on Tuesday.
Most pubs in the country will face hampered trade by the measures.
Those in Tier 2, which will cover 57 per cent of England’s population, will only be able to serve alcohol alongside a “substantial meal” and must obey rules restricting household mixing indoors.
In Tier 3, pubs and restaurants will only be able to offer takeaway and delivery services.
Kate Nicholls, chief executive of trade body UKHospitality, said: “A one-off payment of £1,000 for pubs forced to close does not even count as a token gesture.”
The tiers will be reviewed every fortnight and Mr Johnson promised MPs a fresh vote on whether to keep the system before February 2.
Tory backbenchers were outraged that the Government’s impact assessments on the three-tiered system did not include a detailed breakdown of the economic effects of the measures.
Their anger was further compounded by a report in the Times which revealed the existence of a Whitehall dashboard detailing Covid-19’s impact on almost 40 sectors of the economy.
A red rating, which indicates significant job cuts and revenue losses, was said to be against dozens of them, including aerospace, the automotive industry, retail, hospitality, tourism, arts and sport.
The anger on the Tory benches was set out by prominent backbenchers.
Sir Graham Brady, the influential chairman of the 1922 Committee and a Tory MP in Tier 3 Greater Manchester, said: “If Government is to take away fundamental liberties of the people whom we represent, they must demonstrate beyond question that they’re acting in a way that is both proportionate and absolutely necessary.
“Today, I believe the Government has failed to make that compelling case.”
Former Cabinet minister Damian Green, an MP in Tier 3 Kent, said the plans lacked public support, adding: “I’ve had the most angry emails over a weekend since the Dominic Cummings’ trip to Barnard Castle.”
Labour leader Sir Keir Starmer said the Prime Minister’s strategy posed a “significant” health risk and it was “highly unlikely” to see restrictions eased in parts of the country before Christmas.
He accused Mr Johnson of “overpromising and under-delivering” by pursuing an approach of short-term decisions that then “bump into the harsh reality of the virus”.