No fatalities were immediately recorded but there was severe damage to some buildings, mainly in Durban, capital of KwaZulu-Natal (KZN) province.
“We are yet to receive a full comprehensive report on the impact of these latest heavy rains, but as reports come in a worrying picture is however emerging,” KZN premier Sihle Zikalala said during a press conference.
Torrential rain in late April killed 435 people in floods and landslides. Meanwhile, survivors were left without drinking water for nearly two weeks.
The repairs continue after the storms caused damage worth hundreds of millions of dollars.
The latest floods hit infrastructure, roads, bridges and damaged buildings.
“Some areas are inaccessible and have become islands at this stage,” Zikalala said.
The South African Weather Service put the alert level at the highest. Officials called on residents to stay at home.
Authorities opened 82 reception centres while police, firefighters and rescue workers were ready to respond rapidly to emergencies.
The army has also been called in for reinforcement.
Officials already evacuated elderly people in several villages.
Around 3.9 million people live in Durban, and the Indian Ocean city hosts one of Africa’s main ports.
The rains are expected to continue until Monday, according to forecasts.
South Africa is usually untouched by storms which regularly hit its neighbours like Mozambique and Madagascar.
Picture: Twitter /@PhakamaMthwaka1