The Western Cape has 55 schools affected by Covid-19 cases, while Gauteng has recorded 30.
Eleven of the schools in the Western Cape were closed for cleaning, and were expected to be reopened on Monday.
The provincial education department has shared the guidelines to be followed if a coronavirus case is reported.
The Western Cape says 55 schools have been affected by cases of Covid-19 in the province, while 30 schools in Gauteng have reported cases.
A total of 11 Western Cape schools were closed on Friday due to Covid-19 concerns, but were expected to reopen on Monday.
This was confirmed on Monday by the Western Cape Education Department (WCED), which manages 1 509 schools across the province.
School gates in the province opened for their second week on Monday.
WCED spokesperson Bronagh Hammond said: "Over 99% of our schools were open as of last Friday. Eleven schools were closed on Friday due to cleaning. These schools should be open today [Monday], however, reports have yet to be collated in this regard."
On the number of cases of the coronavirus, she advised: "Last week 55 schools reported new employee cases of Covid-19. This affected 66 employees. In each case, the necessary cleaning must take place. This may or may not affect the school in terms of closure, as some cleaning can take place on a weekend. It depends on the day of confirmation and the times at which the cleaning can take place."
In Gauteng, Education MEC Panyaza Lesufi confirmed on Sunday that 30 schools in the province reported cases of Covid-19. The province manages approximately 2 000 schools.
Lesufi said 26 are public schools, and four are independent. Six of the cases were pupils.
Hammond was asked to detail the steps taken at schools, and explained: "Whenever an employee or learner tests positive or is exposed to someone who has tested positive, the necessary protocols are followed. These protocols can be found in WCED Guideline L: Managing Covid-19 cases in schools."
"Schools have been provided guidelines on cleaning, as well as what to do when there is a positive case of Covid-19 in a school or if someone has been in contact with a positive case of Covid-19.
"Those who have been in close contact (e.g. handshake or hug) with a confirmed positive case are required to self-isolate for 14 days from their last contact with the individual. Those not in close contact do not have to self-isolate.
"If there has been a confirmed case of Covid-19 then the school is required to contact the district for assistance in terms of further cleaning. In all other cases, schools should follow the guidelines and protocols for cleaning as provided," the education department's spokesperson concluded.