Flooding hit several locations in two eastern provinces, two rare tornados were spotted, temperatures plunged and snow fell in some central regions.
At least 11 people died in Eastern Cape, a spokesperson from Nelson Mandela Bay municipality, at the heart of the floods, told AFP.
More than 2,000 people have been evacuated from Nelson Mandela Bay, notably from makeshift homes in the municipality's slums.
Local authorities launched an appeal for donations of clothing, food and blankets.
The provincial government in neighbouring KwaZulu-Natal also said at least 11 people had died in and around the port city of Durban.
Provincial authorities declared a state of alert in KwaZulu-Natal.
A provincial government statement said "55 people suffered minor to moderate injuries and are receiving medical treatment in hospital.
"At least 120 people have been displaced and three temporary shelters have been established," it added.
Durban and its surrounding area in 2022 was the site of the worst flooding in South Africa's history, which provoked mudslides that killed more than 400 people.
Rescue services were deployed in both affected provinces on Monday night.
Homes were flattened, roads flooded and trees felled.
Some places suffered energy blackouts.
The national meteorological institute says South Africa is in the grip of a "cut off low" pressure system, marked by heavy rains and a cold snap that can also bring hail, snow and strong winds.
Heavy rainfall has hit the eastern Indian Ocean coast, and meteorological services have published weather alerts in four of the southern African country's nine provinces.
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