Springbok team doctor Craig Roberts has confirmed that centre Francois Steyn will not play again this year.
Steyn, who missed last weekend's victory over Australia due to an ankle injury, will undergo surgery on Wednesday and is set to be out for three months.
"We've been doing a number of scans and seeing specialists, there is quite few loose bodies in the joint, little pieces bone that in time has broken of ankle," said Roberts.
"Every now and then bones catches into the joint and gets excruciating pain, it can damage the joint.
"It was taken as long term decision, he will be done (operated) on Wednesday, unfortunately keep him out for three months, also for end of year tour."
Young fly-half Johan Goosen sat out of training on Monday because of a bruised heel while full-back Zane Kirchner also did not train due to a bruise on his hip-bone.
"He (Goosen) was comfortable running (on the field), just when he planted his foot for kicking," Robberts said.
"We always knew beforehand that he may be sore, which is why early on we decided to change kicker."