Cars were submerged and scores of people were evacuated during floods in Port St Johns overnight, the Eastern Cape local government ministry said on Sunday.
The residents were evacuated to the local town hall, where they were given blankets and meals, said spokesman Mvusiwekhaya Sicwetsha, but he added that some resident had refused to leave their homes
Local government MEC Mlibo Qoboshiyane appealed to all residents to co-operate.
The department said parts of the R61 between Port St Johns and Lusikisiki had been partially closed following a landslide. Traffic officers were on the scene.
The authorities were also removing a tree which had fallen across another road.
In Soweto, water levels had dropped on Sunday, and there had been no more flood-related emergencies, said Johannesburg emergency services spokesman Robert Mulaudzi.
On Saturday, 136 people were left homeless when their shacks were destroyed by floods. They were taken to the Khayalethu care centre. No one was injured, he said at the time.
Several motorists and passengers had to be rescued when they were trapped on flooded roads in Soweto.
In Diepkloof, two houses were struck by lightning but no one was injured.
Elsewhere in Johannesburg, flooding was reported on the M2 highway.
The SA Weather Service has indicated that the rain and cold weather will last throughout the weekend.
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