President Cyril Ramaphosa offered his condolences while visiting the region. "It was important to come and see what has happened. We pass our condolences to the families of those who have died in this disaster. We are saddened by what has happened here. The loss of life is never easy, especially when so unexpected."
Government officials have added that minors are among those missing, and dozens of other people received injuries and more than 1,000 displaced, so far.
"This situation calls on all of us to pull together as a country to reach out to affected communities," Ramaphosa added.
The extreme weather caused the collapse of buildings and flooded roads, blocked sewer lines and felled electricity towers. A Hindu temple in the city was entirely flooded with water levels of up to 10 meters, AFP reported.
Search and rescue operations, with the assistance of military personnel, are currently underway for missing people who may be trapped under debris, Provincial Minister Nomusa Dube-Ncube told SAFM radio.
Authorities have braced for an increase in the death toll.
According to an AFP report citing Rescue Care spokesman Garrith Jamieson, dozens of people have been hospitalized.
Torrential downpours have flooded the southern and eastern parts of the African nation since Easter weekend.
The South African Weather Service warned that more heavy rain and strong winds are expected until Wednesday.