The 22-year-old was taken off at halftime after trying to run off the injury and scans confirmed a high ankle sprain, leaving Australia coach Michael Cheika with no choice but to rejig his team for next week's Twickenham clash with Argentina.
The back row was an area of strength for Cheika last year when, faced with a surfeit of top-quality openside flankers, he opted for the experimental ploy of playing fetcher Pocock at number eight.
It has been less successful this season, in which the Wallabies have lost six of eight tests, but Cheika persisted with the experiment after losing Pocock to a broken hand two weeks ago.
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"That's two now in that spot," Cheika said. "So we'll see where we end up next week. But (McMahon) was going well when he was on there and that was pleasing."
Cheika's problem is the lack of traditional number eights at his disposal after the international retirement of Wycliff Palu and an injury to Ben McCalman.
Lopeti Timani, who plays at the back of the scrum for the Melbourne Rebels, is in the squad but has played just one test off the bench against Argentina in Perth last month.
Assistant coach Nathan Grey said uncapped loose forward Leroy Houston, who is playing in England for Bath while contracted to the Queensland Reds, could get a phone call as he was part of the squad for the June series against England.
"Leroy, obviously, has been in the programme and sort of knows how we play," Grey told reporters in Johannesburg.
"It's a good option for us to have up our sleeve. He'll be match fit as well so it's a positive."
Cheika put Saturday's defeat to the Springboks down to Australia not taking their chances but was at least happy that the South Africans had failed to cross the tryline, with all of their points coming from the boot of flyhalf Morne Steyn.
Coming after the Wallabies shipped 19 tries in their first five matches of the season against England and New Zealand, Cheika thought it indicated his much-changed squad were gelling.
"It's usually a good sign of a team coming together is defence," he said.
"We've had 10 debutants, a lot of new players in the squad and we're building our team harmony, our friendships and the things that happen off the field.
"Because that's what defence is, you want to tackle and defend for each other on the field."
(Reporting by Nick Mulvenney in Sydney,; Editing by Peter Rutherford/Sudipto Ganguly)
