The disaster followed a powerful meteorological system which brought heavy rains, strong winds and even snow in certain parts of the Southeast early Tuesday.
The city of Mthatha was among the most affected, flood waters took a school bus, killing six students and two adults.
The rescue teams found the bus empty on Wednesday and confirmed that four students are still missing.
Hundreds of families have been moved and dozens of schools and hospitals have been damaged.
The authorities say that research operations will continue and that the total extent of the damage is still unknown.