The 20-year-old, already capped by the Springboks and hailed as a brilliant prospect, slipped while training with the Cheetahs in Sydney ahead of Saturday's Super Rugby game against the Force in Perth.
"He slipped while kicking balls during practice," Cheetahs manager Eugene van Wyk told South African media. "It was a freak accident, there was no one near him at the time. He was just running when it happened."
Goosen will fly back to Bloemfontein on Thursday for surgery on his right knee, his franchise said, and faces some six months on the sidelines.
Goosen debuted for South Africa last September after recovering from a shoulder injury that cut short his Super Rugby season. He later suffered ligament damage in his left knee that sent him back to the treatment table and had only recently recovered.
The Cheetahs are seeking an unprecedented third successive away win in Super Rugby following victories over the Highlanders in New Zealand a fortnight ago and Waratahs in Sydney on Saturday, where Goosen had played a significant part.