Cooper is out injured with a knee problem and Beale will step into the playmaker role in his 30th Test. Cooper has also been contacted by the Australia Rugby Union after a series of negative Tweets about team morale.
"The (jersey) number might be new but his role within the game won't be," Deans said of Beale in a statement.
" Although his season hasn't been without challenge, Kurtley stepped up with his involvements on the Gold Coast, making a difference when he was on the field.
" He's brought that enthusiasm forward with him since we've been in South Africa, has worked hard on the training track, and is excited about the opportunity ahead. He has good memories from some of his experiences over here," Deans said.
Berrick Barnes will start at fullback and assume the kicking duties, Deans said. Lock Nathan Sharpe, in his 110th Test, continues to captain a side hit hard by injuries.
Sharpe will join former openside flanker George Smith as Australia's most capped forward, and a personal milestone awaits front-rower Benn Robinson, who will be playing his 50th test.
Second rower Kane Douglas has retained his place but Sitaleki Timani's return from a hamstring strain will have to wait after medical staff judged he was not fit enough.
Australia beat the Springboks 26-19 earlier this month in Perth but Deans warned against complacency, especially at the Loftus Versfeld Stadium in Pretoria where they have never won.
"They are proud men, and they don't lose at Loftus very often," Deans said of the Springboks.
"While they are coming off a tour which would have disappointed them, they were in both contests and will feel that they could have won on both occasions.
" That will only spur them on, as will the atmosphere which is always electric for test matches in Pretoria."
Deans is also wary of the Springbok goal - kickers such as inside centre Francois Steyn.
"Discipline is always key, but there's no doubt about its importance when you play South Africa as they always have goal-kickers who can routinely kick goals anywhere on our side of halfway, or even from 60 metres at altitude in Francois's case."
Australia team to face South Africa: 15-Berrick Barnes, 14-Dominic Shipperley, 13-Adam Ashley-Cooper, 12-Pat McCabe, 11-Digby Ioane, 10-Kurtley Beale, 9-Nick Phipps, 8-Radike Samo, 7-Michael Hooper, 6-Dave Dennis, 5-Nathan Sharpe (captain), 4-Kane Douglas, 3-Ben Alexander, 2-Tatafu Polota Nau, 1-Benn Robinson.
Replacements: 16. Saia Fainga'a, 17-James Slipper, 18-Rob Simmons, 19-Scott Higginbotham, 20-Liam Gill, 21-Brett Sheehan, 22-Anthony Fainga'a