There is also doubt over winger Digby Ioane (kneecap), back-rower Radike Samo (shoulder) and hooker Tatafu Polota-Nau (neck/shoulder).
The Wallabies will send Melbourne Rebels lock Cadeyrn Neville and Queensland back Luke Morahan as reinforcements to Argentina.
The Springboks deserve credit after ending their five-game losing streak against the Wallabies, with veteran winger Bryan Habana scoring a hat-trick in the five-try haul.
Their smothering defence and ferocity at the breakdown set up the win, with the Australians, who hoped to post their first victory at Loftus, getting little quality ball or position to attack.
But it was difficult to read much into the game because of the "carnage", as Deans called it.
The coach was left fuming by the substitution confusion, which meant they were down a man for the final eight minutes, their last two scrums were uncontested and it was prop Benn Robinson who threw the ball at a lineout.
Deans said the fourth referee gave them the green light to replace the injured Polota-Nau and they called him off the ground but, before Saia Faingaa could go on, they were told he couldn't.
"We attempted to return him [Polota-Nau] to the ground and they said no, he's off for injury, so that was a source of frustration."
Australia trailed 14-3 at halftime but the margin could have been much larger but for the Springboks missing two penalty kicks and having two tries disallowed.
Losing Barnes put a lot of pressure on five-eighths Kurtley Beale, who did well in the circumstances.
South Africa 31
Australia 8
- AAP
