"Regrettably, so far four people have been confirmed to have lost their lives," the KwaZuly Natal province's disaster management department said in a statement.
Three died in Durban and a fourth in wider KwaZulu-Natal, it said, adding that a fifth person was missing and more than 150 were homeless.
Powerful winds and rainfall damaged roads and flooded houses and sewer systems, followed by a tornado that struck north of the port city of Durban on Tuesday.
The rainy season in KwaZulu-Natal usually runs from November to March, and exceptional rainfall at this time of year is unusual, it said.
"We are experiencing firsthand the true effects of climate change during the winter season," the department said.
In April 2022, the province was hit by the worst floods in living memory, suffering the loss of more than 400 lives in Durban and surrounding areas.
Experts have warned that floods and other extreme weather events are becoming more powerful and frequent as the world gets warmer.