Kolisi suffered a knee injury as Australia rallied from 22 points down in a stunning second-half display and is out of the second test in Cape Town on Saturday and likely the two-match tour to New Zealand that follows.
Loose-forward Pieter-Steph du Toit suffered a concussion in the weekend loss and will also miss the second game as he goes through return-to-play protocols.
Both wings from the loss, Kurt-Lee Arendse (knee) and Edwill van der Merwe (ankle), are also out of this coming weekend.
That should be tempered by the return from injury of experienced wing Cheslin Kolbe. Inside centre Damian de Allende, an important cog in the backline, is also set to be fit after missing Saturday's loss.
Coach Rassie Erasmus said the team are aware of their shortcomings at Ellis Park as they tried to move the ball too expansively and were picked off by a clinical Australia.
"We had a proper meeting and the feeling is frustration," he said on Monday. "But at least we know what we did wrong. That's the most important thing. They totally outplayed us.
"If you play beautiful rugby and you lose, you lose. If you play boring rugby and you win, then people are happy. We were totally on the wrong side of that balance on Saturday, and that is not because (attack coach) Tony (Brown) coaches that way.
"You tend to think things are easy and there is so much space. Then a proud country like Australia take their opportunities."
South Africa will name their second test side on Tuesday.
