A motion to renew emergency coronavirus powers was approved by Parliament after the Health Secretary announced that MPs are to get the final say on "significant national measures" related to the crisis.
Matt Hancock proposed an extension to the Coronavirus Act, but said if MPs back its renewal they will be consulted on major rule changes and, where possible, will get to vote on measures before they are implemented.
But he said ministers must retain the ability to impose measures with immediate effect as the government seeks to respond quickly to the pandemic's ever-changing developments.
By offering MPs a vote on major measures it appears the government bowed to significant pressure from more than 50 Tory rebels who were planning to back an amendment to the Coronavirus Act which would have granted them more power over decision making.
The amendment, tabled by Sir Graham Brady, chairman of the influential backbench Tory 1922 Committee, had enough support to inflict a defeat on Mr Johnson if opposition parties backed it.
The health secretary told MPs: "Today I can confirm to the House that for significant national measures, with effect in the whole of England or UK-wide, we will consult Parliament - wherever possible we will hold votes before such regulations come into force.
"Of course responding to the virus means that the Government must act with speed when required and we cannot hold up urgent regulations which are needed to control the virus and save lives."
MPs voted by 330 votes to 24, majority 306 to extend the Act - a law giving the government extra powers to implement mitigating measures - and will not vote on amendments.
Health Secretary Matt Hancock tweeted: “I’m pleased the Coronavirus Act has been renewed with an overwhelming majority 306. The Act is crucial for our strategy: to suppress the virus, supporting the economy, education, and the NHS until a vaccine can keep us safe.
Sir Graham praised Mr Hancock for being "prepared to listen" regarding the importance of parliamentary scrutiny.
It appears the government decided to allow votes on significant measures in order to keep the group of backbenchers on side.
He said: "Members on both sides of the House understand the importance of ministers having the freedom to act quickly when it's necessary, but we are grateful that he and other members of the government have understood the importance of proper scrutiny in this place and the benefits that can bring to better government as well."
The government was spared the prospect of defeat thanks to Speaker Sir Lindsay Hoyle, who said the debate of any amendments could undermine the rule of law.
Ahead of PMQs Sir Lindsay indicated his support for MPs who feel they have been shut out of the process of scrutinising regulations introduced to limit the spread of the virus by curbing people's freedoms.
"All too often, important statutory instruments have been published a matter of hours before they come into force and some explanations as to why important measures have come into effect before they can be laid before this House has been unconvincing and shows a total disregard for the House," Sir Lindsay said, just before Mr Johnson faced Prime Minister's Questions in the Commons.
He called on Boris Johnson's Government to "rebuild trust" with the Commons "and not treat it with the contempt that it has shown".
As MPs went to vote, Mr Johnson fronted a Downing Street press conference with England's chief medical officer Professor Chris Whitty and chief scientific adviser Sir Patrick Vallance.
Last week, the scientists published a projection that showed the number of new cases could reach 50,000 per day by mid-October, if cases doubled every seven days.
If such a projection was coming true, the UK would now be seeing around 12,000 new cases reported each day, but the latest daily total was 7,143.