The gold and PGM miner, which this year took over US company Stillwater, has put the Cooke gold mine, near Johannesburg, onto care and maintenance and threatened to do the same at the Beatrix mine, further to the south.
The job losses were announced days after Sibanye said it would lose in the region of US$350 million in 2017, which it put down to "occupational healthcare claims", restructuring and integration costs from the Stillwater merger, and a less-favourable exchange rate.
In a statement, the company said Cooke was not profitable any longer.
"It was not possible to define realistic arrangements to operate Cooke 1, 2 and 3 on a profitable basis," the company said.
The mine produced 182,000 ounces of gold in 2016, when the Cooke 4 shaft was still part of the operation.
The processing plant can take tailings and will stay open, employing 132 people, and Sibanye said it had transferred 1,510 workers to other operations.
Investors were positive on the job cuts, with shares up 2% to $1.32 per share on the news.
In May, Shares in Sibanye almost halved to $1 per share after a $1 billion rights offer to pay for part of the Stillwater deal was approved.
Sibanye CEO Neal Froneman said he was happy with how the layoffs had gone.
"The decision to restructure was not taken lightly, but it is pleasing to note that we have managed to ameliorate job losses through the consultation process," he said.
"We preserved employment for 3,282 people, while ensuring the sustainability of our remaining operations and thereby securing over 60,000 jobs in South Africa."
Earlier in October, Sibanye was celebrating the early opening of the Blitz PGM project in Montana, US, a $250 million extension of the Stillwater mine.