In Eastern Cape province, "the death toll is currently sitting at seven," 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.
Near the port city of Durban in neighbouring KwaZulu-Natal province, "five people have sadly lost their lives in the eThekwini Metro, which has been hardest hit, and dozens of people are being treated for injuries in health care facilities", the provincial government said in a statement.
Provincial authorities declared a state of alert in KwaZulu-Natal.
Durban and its surrounding area was in 2022 the site of the worst flooding in South Africa's history, which provoked mudslides that killed more than 400 people and caused several millions of dollars worth of damage.
Rescue services were deployed in both affected provinces on Monday night.
Images supplied by authorities show flattened homes, flooded roads and felled trees.
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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