Cooper will miss the Tests in South Africa and Argentina after scans revealed he needed a further operation on the knee he had reconstructed after the World Cup last year.
Deans will instead trust in the versatility of his other backs with three members of the 28-man squad - Berrick Barnes, Kurtley Beale and Mike Harris - all familiar with the fly-half position.
Barnes, who started at full-back in the comeback victory over Argentina last week, stood in for Cooper for this year's Test series against Wales and the opening match of the championship against the All Blacks.
Beale has played mostly at fullback for the Wallabies but started his career in the number 10 shirt and put in some impressive displays for the Melbourne Rebels in the pivot role this year.
Harris has played two of his three Tests at inside centre but came on as replacement at fly-half to kick the winning points when the Wallabies beat Wales 25-23 in Melbourne in June.
Cooper joined a long injury list already featuring his halfback partner Will Genia, openside flanker David Pocock, back James O'Connor and World Cup captain James Horwill.
There was better news about hooker Stephen Moore and lock Sitaleki Timani, who are able to travel after recovering from hamstring injuries, while winger Dom Shipperley has got the all clear after dislocating a finger against the Pumas last week.
The squad departs for South Africa on Thursday before playing the Springboks in Pretoria on September 29. Their final match of the championship is against Argentina in Rosario a week later.
Forwards: Saia Faingaa, Stephen Moore, Tatafu Polota-Nau, Ben Alexander, Paddy Ryan, James Slipper, Benn Robinson, Rob Simmons, Nathan Sharpe, Kane Douglas, Sitaleki Timani, Scott Higginbotham, Radike Samo, Michael Hooper, Liam Gill, Dave Dennis
Backs: Nick Phipps, Brett Sheehan, Ben Tapuai, Anthony Faingaa, Pat McCabe, Digby Ioane, Dom Shipperley, Nick Cummins, Adam Ashley-Cooper, Kurtley Beale, Berrick Barnes, Mike Harris.
- Berrick Barnes
- Kurtley Beale
- Mike Harris