Thousands of grade seven and grade 12 students had been preparing to attend the first classes in the country after two and a half months of home-schooling to limit the spread of coronavirus.
The education department announced late on Sunday that it had postponed the resumption date to June 8, saying the extra week would serve to better prepare facilities and train staff.
"It became clear that the sector was at different levels of readiness," Education Minister Angelina Motshekga said at a press briefing on Monday.
"There were key factors around safety for the coronavirus which have not been satisfied, like water."
Motshekga apologised for the inconvenience caused by the "very late" decision, which was made on Saturday.
"Some learners were on their way to school," she said, adding that some principals had not been informed on time.
President Cyril Ramaphosa said teachers, parents and governing bodies had agreed not to reopen schools "until all the necessary precautions" were in place.
"Several of these stakeholders... have expressed concern about the state of readiness in many schools," the president said in his Monday morning letter to the nation.
"We have heard them, we welcome their contributions and are taking steps to address their concerns as well as proposals."
Only the Western Cape province, home to South Africa's second biggest city Cape Town, deemed schools prepared enough to reopen on Monday as planned.
A handful of worried parents took to the streets in small groups, calling on the government to prioritise the "lives of learners" over completing the curriculum.
Last week, teacher unions and governing associations had urged staff to ignore the government's order to resume class, citing a lack of personal protective equipment.
South Africa entered level three of a five-tier coronavirus lockdown on Monday, marking a further easing of restrictions since the start of the nationwide shutdown on March 27.
The country has the Africa's highest number of confirmed coronavirus cases, with more than 32,600 infections and at least 683 deaths recorded to date.