Another 150,000 were either in cities with high virus rates, or enrolled in classes which did not open due to low vaccination rates.
Israel has been offering vaccines to those aged 12 and up, and has refrained from opening high school classrooms in which fewer than 70 per cent of pupils are vaccinated.
On Tuesday, the health ministry had confirmed 10,947 new virus cases for the previous day, the highest ever daily tally.
Prime Minister Naftali Bennett defended the government's decision to open schools despite the leap in infections, stressing that he wanted to avoid measures that would have kept children, and their parents, at home.
"We learned this year that there is another important thing," he said at a school in the southern city of Yeruham.
"And that is livelihood, to make sure that all the people of Israel can work and earn a decent living, even during the coronavirus, because it is a sacred thing."
Before Wednesday's school reopening, Israeli conducted hundreds of thousands of serological tests on children under the age of 12 to determine if they had developed antibody protection after contracting COVID-19.
The government also distributed millions of antibody tests for pupils to take at home prior to the first day of school.
About 60 per cent of Israel's 9.3 million residents have received two shots of the vaccine, including 80 per cent of adults.
In December, Israel was one of the first countries to launch a national vaccination campaign, which brought daily infections down to a trickle and, in June, allowed the lifting of nearly all pandemic restrictions.
Several measures have since been reimposed, including indoor mask-wearing, limits on gatherings and the need to present proof of vaccination for entry to certain facilities.