Police said Jooste succumbed to a gunshot wound in hospital, with local media reporting he shot himself at his home in the southern town of Hermanus.
“The circumstances surrounding his death are being investigated,” police spokesperson Andre Traut said.
It came a day after the 63-year-old was ordered to pay a $25m (£20m) fine.
The country’s financial regulator said Jooste had played a role in the publishing of misleading financial statements about Steinhoff International Holdings.
The retailer has suffered heavy losses, as have investors in South African pension funds, since an accounting scandal broke in 2017.
Jooste had resigned as chief executive, but denied any knowledge of accounting fraud.
Prior to that, the businessman had acquired billions of dollars’ worth of high street retailers across Europe including the UK-based Poundland.
He had also been fined for insider trading in 2020.