The disaster followed a powerful weather system that brought heavy rain, strong winds, and even snow to parts of the southeast early Tuesday.
The town of Mthatha was among the worst hit, with floodwaters sweeping away a school bus, killing six pupils and two adults.
Rescue teams found the bus empty on Wednesday and confirmed that four students remain missing.
Hundreds of families have been displaced, and dozens of schools and hospitals damaged.
Authorities say search operations will continue, and the full extent of the devastation is still unknown.