The precipitation cut off all road links between Johannesburg and Cape Town, causing huge traffic backlogs, though main highways linking the north and south of the country were reopened on Sunday afternoon, said Road Traffic Management Corporation spokesperson Ashraf Ismail.
Dozens of trucks had been stuck on the routes after heavy snow had forced them to close on Saturday.
Soon after traffic was opened, around 500 trucks that had been held up in Johannesburg began the trek toward Cape Town, Ismail said.
Over 100mm of rain fell over the area in three days, with more heavy showers predicted through Sunday night.
Thousands of people were moved to community centres as floods hit southern city Port Elizabeth, said municipal spokesperson Kupido Baron.
"Showers are expected within the next few hours according to information received from the South African Weather Service," said Baron.
Port Elizabeth residents were cautioned and advised to avoid going to low lying areas as there had been two possible drowning incidents, he said.
He said the water level of the Swartkops River was also rapidly rising.
More roads were being closed as a result of rising water levels.
These were the Third Avenue dip (Newton Park), Seaview Road, and Genadendal and Kruisriver roads in Uitenhage.
"We assisted more than 2 000 people," he said, with mattresses, soup and blankets given to families housed in community centres.
Police were also looking for two people who ignored a ban and rowed across a flooded road in an inflatable rubber boats. – Sapa-AFP