Coach Heyneke Meyer, mindful of the big World Cup picture, let the Aussies back into the game. But don't be fooled by the scoreboard, and even Australia's goalkicking is struggling for accuracy and range.
Most of Australia's best performers came off the bench. James Horwill, David Pocock, Nick Phipps and Matt Toomua either outplayed or looked better prospects than Will Skelton, Scott Higginbotham, Will Genia and Matt Giteau. An imploding Aussie scrum suddenly went gangbusters, but only after the substitutions.
The dilemma for Cheika's Australia - who face England and Wales in their World Cup pool - is that Cooper is the key to spreading the ball against big opponents and he throws a decent long pass on the run.
But ... Cooper still doesn't have a head for tests. Even an easy kick at goal went so wide it was actually funny. For every rabbit Cooper can pull out of a hat - he helped create a try to Adam Ashley-Cooper - there's a truck load of missing bunnies.
Cooper has been around long enough to delete the nonsense out of his game, know how to work the percentages even if they are a bit different from the rest. Instead, he is still capable of whacky plays that get his team into unimaginable trouble. The Cooper Classic Moment this time came on the halftime hooter, when he flung a pass behind his own back to no one inside his 22. Desperate Wallabies defence saved the day but had the Springboks profited from Cooper's brain snap, test over.
It's hard to work out how Australia won this game, or maybe how the Springboks managed to throw it away. Veteran loose forward Schalk Burger was immense as the Boks dominated Australia. Even the visitors' backs showed a creative sharpness banned from South African rugby for a century or so.
Pocock got it bang-on though. The Aussies must review this game as if they lost and there's an easy way for Cheika to do that, by imagining the loopy Cooper pass led to a Springboks try.
There are reports that Cooper is about to re-sign with the ARU until 2019. If so, we get the last laugh on the famous George Gregan line. Four More Years, Australia.