Cooper requires surgery to clean up a small chip of articular cartilage in his right knee - the same knee he damaged in the 2011 World Cup.
The 24-year-old tore his ACL in the Bronze Medal Match with Wales last October and missed the majority of the Super 15 campaign.
But his current injury is far less serious and he could even return for Australia's autumn tour of Europe when the Lions' next opponents face France, England, Italy and Wales.
"While the injury will require an operation to clean up and is to the same knee that was operated on after last year's Rugby World Cup, it is not a long-term injury and so may not rule Cooper out of the (November tour)," read a statement from the Australian Rugby Union.
"A decision on the fly-half's availability for that trip will be made once his rehabilitation is underway."
Cooper's chances of facing South Africa next weekend were looking a little slim regardless of his injury after another disappointing showing for his country.
The Reds playmaker saw a charged-down kick lead to an Argentine try on the Gold Coast as he again failed to ignite a Wallaby backline that was considered the best in the world last season.
Head coach Robbie Deans hinted that Cooper may be replaced by Berrick Barnes or Kurtley Beale for the trip to Pretoria, with the Kiwi admitting that he and his staff would be considering their combinations carefully before the Round 5 encounter.
"That (charged-down) kick was disappointing. Quade's a better player than that," said Deans.
"We shouldn't underestimate the time it takes to comeback from a significant injury. Maybe, that's in the back of his head. I don't know.
"Some of the unforced errors you wouldn't expect."
News on Cooper's knee is the latest in a long line of setbacks for the Wallabies, who are already without captain James Horwill and stand-in skippers David Pocock and Will Genia, as well as the likes of back rowers Ben McCalman and Wycliff Palu.
Utility back James O'Connor hasn't featured in the defeats to the All Blacks and the wins over the Springboks and Pumas, while wings Drew Mitchell, Cooper Vuna and Joe Tomane are all also sidelined.