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The council said the 34-year-old man, who worked at an operation in Mpumalanga province, had fallen ill during the lockdown period and had no contacts at work immediately prior to his illness as the operation was closed at the time.
South Africa's mining industry was stopped as part of a nationwide lockdown in March to prevent the spread of the global pandemic.
Operations were allowed to ramp up to a 50% workforce capacity in April and must now adhere to new COVID-19 safety guidelines after a union sought binding regulations to protect mineworkers.
The minerals council said on Friday there were 23 positive cases of COVID-19 among industry employees and 10 had recovered.
It extended condolences to the 34-year-old man's family and colleagues.
The council said about 165,000 employees had been screened and 877 tested.
The council's head of health Dr Thuthula Balfour said there was an increasing trend of regional transmission, compared with the industry's initial cases which were reported largely at corporate offices or among professionals who had travelled internationally.
"Our understanding is that none of the 21 cases are as a result of on-mine transmission," Dr Balfour said.
"Around 40% of the positive cases are women."
The council put the number of positive cases in South Africa on Friday at 12,739, which has since grown to 15,515 and 264 deaths, according to Johns Hopkins University.
The figures mean South Africa has the highest number of cases on the continent.