They will remain open exclusively to vulnerable students and children of key workers until after the February half-term, with all other teaching to move online.
However, early years settings, such as nurseries, will still be accessible to families under the new restrictions, while university lessons will remain online until mid-February for all except future critical worker courses.
Announcing the plans for schools, the PM said: “We recognise that this will mean it is not possible or fair for all exams to go ahead this summer as normal.”
Education Secretary Gavin Williamson will work with regulator Ofqual to put in place “alternative arrangements”, Mr Johnson stressed.
He added: “We will provide extra support to ensure that pupils entitled to free school meals will continue to receive them while schools are closed, and we will distribute more devices to support remote education.”
The decision to close schools came after education unions warned that bringing all pupils back to class could fuel the pandemic and put teachers at “serious risk” of falling ill amid the new variant of Covid-19.
The Government’s “chaotic” handling of the opening of schools has caused confusion for parents and teachers, according to the bodies representing school staff and headteachers.
All of London’s schools and those in some surrounding areas worst hit by the virus had not yet returned to class, but primary school pupils elsewhere in England began heading back to school on Monday.
Secondary schools and colleges had already been told they would have a staggered return, with those taking exams expecting to return on January 11 and other year groups on January 18.
But now all students in England – except children of key workers and vulnerable pupils – will learn from home until the February half-term.
Mr Johnson said he recognised the “inconvenience and distress” that the late change would cause millions of parents and pupils up and down the country.
Speaking on Monday, he said: “Parents whose children were in school today may reasonably ask why we did not take this decision sooner.
“The answer is simply that we have been doing everything in our power to keep schools open, because we know how important each day in education is to children’s life chances.”
Mr Johnson added: “And I want to stress that the problem is not that schools are unsafe for children – children are still very unlikely to be severely affected by even the new variant of Covid.
“The problem is that schools may nonetheless act as vectors for transmission, causing the virus to spread between households.”
Last month, Education Secretary Mr Williamson gave an “absolutely” cast-iron guarantee that exams in England would not be cancelled this academic year.
He made the pledge in December as part of a package of measures designed to compensate exam students for disruption to their schooling during the pandemic.
Pupils in England were told they would be given advance notice of some topics ahead of their tests and they would be allowed to take in exam aids, like formula sheets, to ensure this cohort of students is not disadvantaged.
Now the Department for Education and Ofqual will discuss what shape GCSE and A-level assessments will take this summer.
Geoff Barton, general secretary of the Association of School and College Leaders (ASCL), said: “This decision clearly raises a question about GCSEs, A-levels and other exams which are due to take place in the summer.
“This new lockdown will be disruptive to learners who have already been hugely disrupted. Schools and colleges are very worried about how exams can be made fair in these circumstances.”
Meanwhile Patrick Roach, general secretary of the NASUWT teachers’ union, said: “Given the scale of the difficulties faced, the Government is right to look at alternative plans for exams this summer.
“It is essential that the Government works with the profession on these plans and does not repeat the mistakes of last summer. The Government must also confirm that it is cancelling statutory tests for primary school pupils.”
Dr Mary Bousted, joint general secretary of the National Education Union (NEU), said: “No one wanted schools and colleges to be shut again but the evidence clearly pointed to the necessity for this to happen weeks ago.
“Why Boris Johnson allowed such confusion and chaos to build up around school openings before making this belated, blindingly obvious decision is beyond belief.
“Government must take responsibility for this closure because it has allowed Covid-19 to become, again, out of control.”
Just hours before Mr Johnson’s speech, Nicola Sturgeon ordered schools in mainland Scotland to stay closed to most pupils until February 1 at the earliest.
In Wales, all schools and colleges will move to online learning until Monday January 18.
Labour ministers responded to the Prime Minister’s announcement with fury and disbelief as they called for urgent plans to be laid out for students and teachers.
Shadow foreign secretary Lisa Nandy tweeted: “This is beyond chaos. How can learning go online tomorrow when teachers were told to spend the last two weeks planning for reopening?
“What will replace exams? And since the PM was told by SAGE that this would almost certainly be necessary on 22 December why is he so unprepared?”
Shadow schools minister Wes Streeting tweeted: “Johnson just cancelled exams without any plan to replace them. This will cause additional anxiety for pupils and teachers.
“We’ve called for months for a Plan B in case exams couldn’t take place. He should be announcing that plan, not starting with a blank sheet of paper.”