The six-year research project along the country's coastline revealed that only between 353 and 522 of the sharks are still alive, half the level previously thought.
"The numbers in South Africa are extremely low. If the situation stays the same, South Africa's great white sharks are heading for possible extinction," said study author and Stellenbosch University researcher Sara Andreotti.
Scientists conducted the census by collecting biopsy samples and photographs of dorsal fins of the great predators, including in the Gansbaai area, near Cape Town, a hotspot for shark cage diving.
The study published in the journal Marine Ecology Progress Series also blamed shark nets, ocean pollution and baited hooks on the eastern seaboard of South Africa for the dwindling numbers.
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"The chances for their survival are even worse than what we previously thought," said Andreotti.
About 333 of the sharks are thought to be capable of breeding.
Although the great whites population has dropped off South Africa, the report said the sharks were still found in large numbers off the coast of Canada, Australia and the United States.