Nearly 200 staff and students have been infected in the greater Seoul area over the past two weeks.
Remote learning will continue until 11 September, the Ministry of Education said.
Health authorities have warned that the country is on the brink of a nationwide outbreak.
All students in the greater Seoul area, home to over 25 million people, will now take classes online with the exception of those in their final year of high school who are due to take university entrance examinations in December.
Schools with fewer than 60 students and special education schools are allowed to choose whether to follow the ministry's guidelines, the Korea Times said.
Most of South Korea's schools reopened in stages between 20 May and 1 June after cases in the country appeared to fall.