Australia conceded a handful of tries to see their five-match winning run against the Springboks come to an abrupt end and they suffered a whole host of injuries in the process.
But Deans was able to find some solace in the performance of Kurtley Beale, who didn't look out of place in his first start at fly-half.
"I thought Kurtley was outstanding in difficult circumstances," said Deans.
"He was able to create some momentum on occasions and kicked very well.
"As a first hit out at five-eighth in a tough situation when down to 14, 13 and 12 upright men on the field, he created quite a bit with his carries and putting others into gaps."
The Wallabies were outplayed for most of the match but Beale did at least threaten to inspire a mini revival when the game got looser late on.
The Rebels playmaker, who won his country's Player of the Year award from full back last season, showed his class when he set up Australia's solitary try.
Beale hardly had any decent attacking ball at Loftus Versfeld but he did demonstrate how dangerous he can be when he stood up his man and created a simple score for replacement Mike Harris.
He then produced another moment of magic by catching his own chip ahead and finding a sensational offload but the brilliance went unrewarded and the Wallabies left the Republic battered, bruised and beaten.
Injuries to the likes of Adam Ashley-Cooper, Radike Samo, Tatatfu Polota-Nau and Digby Ioane will force the Wallabies into even more changes on Saturday but Beale is almost certain to continue in the No10 shirt.
With fly-half rival Berrick Barnes suffering a punctured lung against South Africa, Beale faces little competition for the role as the Wallabies prepare to take on Argentina in Roasrio.
Barnes lost out to Beale for the playmaker's role in Round 5, while controversial colleague Quade Cooper is currently sidelined with a knee injury.
Harris is the sole alternative for the pivotal position but, despite injury worries out wide, it would be a major shock if Deans was to reshuffle his backline and start Beale at full back rather than fly-half.
And with Cooper's future with the Wallabies currently unclear after his comments on Australia's approach and a 'toxic environment' with the camp, Beale could suddenly find him himself as favourite to run the Wallaby show when the Lions come calling next summer.