Quade Cooper has capped an incredible Wallabies return, kicking a match-winning penalty after the siren to beat South Africa 28-26 in his first Test for more than four years.

A shock call-up to face the world champions, Cooper kicked a perfect seven-from-seven penalties and a conversion as the hosts won a scrum penalty in the final 20 seconds.

That set up a potential matchwinner from 40 metres out and 12 metres from touch that the maligned playmaker, now playing second-tier rugby in Japan, calmly slotted.

Cooper, 33, said that after previously kicking one from a similar spot he knew he had the distance.

"I looked at it and had a little chat to myself and said 'is this your ego saying you want to take the kick or is it what's in the benefit of the team'," Cooper told Stan Sport.

"I had a little chat to Hodgey (Reece Hodge) as well and he backed me, so you know your peers are backing you, you got to back yourself as well."

Cooper was understated in his Wallabies comeback in the Rugby Championship clash on the Gold Coast, reeling in his long passing game but still providing good service to his outside men in a poised display the side needed after three straight losses to New Zealand.

Cooper's pass to Samu Kerevi put him into space in the first half, the centre's step inside and long pass finding Andrew Kellaway for the game's first try.

A scrum penalty offered Cooper another three points that built a 19-11 halftime lead - their first in seven Tests this year.

The Springboks turned pressure into points, Bongi Mbonambi's first-half try and Malcom Marx's second-half double all coming from rolling mauls.

Marx's second put them in front for the first time in 71 minutes, but another missed kick - their side's fourth of the night- meant it was just a solitary point in the contest.

The Wallabies looked for a reply in the final three minutes but appeared to miss their chance when Reece Hodge knocked on after Michael Hooper's line break.

Hodge then put up a bomb to give away possession in the final minute, but they rescued it with another strong scrum to set up the fairytale finish.

There were four yellow cards, South African captain Siya Kolisi and Wallabies hooker Folau Fainga'a both sent for dangerous tackles while Willie Le Roux was deemed to knock a pass down deliberately and Matt Philip binned for pulling down another South African maul.

Cooper said he felt "at peace" with the game after a tumultuous career that saw him exiled from the Reds and also unwanted by former Wallabies coach Robbie Deans.

"This is a game of rugby. When we put that in perspective and understand that we're going to walk off this field win, lose or draw ... it's not going to be the end of the world," he said.

"There's so much more to life than just the result of a football game and when you can understand that, that's when you when you feel at peace with the game, and with everything else around us."