Inspirational flanker Duane Vermeulen was a thorn in New Zealand's side at Wellington, but the No8 injured his ribs in Cape Town and must be a question mark for Ellis Park.
"He is one of the leaders in the team and a player who is in great form at present," said coach Heyneke Meyer.
South Africa were also forced to counter some "transformation" controversy in the lead-up to the Wallabies match.
Flanker Teboho Mohoje was selected to start and there was a clear inference in some quarters of the media that he was picked to appease the concerns of those like Bishop Desmond Tutu, who have criticised South African Rugby for the lack of black players in the Springboks.
"I thought a couple of the guys really got insulted by the media [last] week, that they got selected only on colour," de Villiers said. "The display showed that each player was selected on merit - hopefully that's the last time we read something like that."