The weather cleared up in most parts of the country by Saturday, the SA Weather Service said.
“No heavy rain or flood warnings have been issued,” said forecaster Bongani Cidi.
He said rainfall was expected in parts of the Western Cape and the Northern Cape on Sunday.
A 60 percent chance of rain was forecast for Monday in Gauteng, Mpumalanga, the Free State and North West.
This week, flooding in parts of the country led to people being swept away and displaced.
Three boys went missing in Mamelodi East, Pretoria, on Monday and one of their bodies was found on Saturday, the city of Tshwane said.
The deceased boy was found underneath a tree, spokesman Blessing Manale said.
The search for the remaining two boys was continuing.
The bodies of three others, who were swept away by floods in the North West, had also been recovered.
Lesiba Kgwele, spokesman for North West premier Thandi Modise, said the body of a seven-year-old boy was recovered in Mogwase and two missing men were found in Marikana.