Habana suffered a concussion on Saturday in the Springboks' 21-20 win over New Zealand in Rustenburg and was on Tuesday ruled out of this weekend's game.
"Bryan is out with concussion," coach Jake White told journalists after practice.
White hinted that he may try Wynand Olivier - normally a midfielder at wing - as a replacement.
Jaque Fourie should move back to outside centre after one game at fullback to re-unite with Jean de Villiers in the midfield.
"There are opportunities with backs that have just joined us and it is nice that we can try a thing or two this Saturday," White added
"Josh Lewsy plays centre for Wasps and wing for England. Lote Tuqiri has played at centre and wing for Australia.
"Where the backs are playing now is one of the secrets of rugby going forward. No matter what number you play you can interchange the backs but you have to make sure you have the right options."
Os du Randt missed the training session but White said there was no cause for alarm.
"Os has just a bump, the tractor is just a bit tired. He will play," he said.
White added that the altitude was unlikely to have an effect on the game.
"A lot is made of the highveld," he said. "Australia now have decided to train in Johannesburg which is the first time ever. It must be an advantage but I don't think that is a major factor look what the All Blacks did to us at Loftus two weeks ago."
The Springboks are due to name their side on Wednesday.