Eddie Jones' return as Australia head coach ended in a chastening defeat as Kurt-Lee Arendse's hat-trick led South Africa to an opening Rugby Championship victory in Pretoria.

Overall there were few positives for Jones in his first match back in charge of the Wallabies since 2005, although they did score an early try through wing Marika Koroibete and debutant Carter Gordon crossed late on.

The Wallabies took the lead when Koroibete powered over in the eighth minute after a swift passing move out wide.

South Africa hit back through a Manie Libbok penalty and rarely looked back thereafter.

Arendse went over after some scrappy build-up before driving through to complete the turnaround after an effective line-out on the half-hour mark. Libbok converted both tries.

Ten minutes after the break, Arendse grabbed his third try of the match, touching down in the corner after a video review for a possible forward pass by Lukhanyo Am.

Australian hooker David Parecki was sent to the sin bin after collapsing a maul as South Africa were awarded a penalty try, before Libbok was denied a fifth score after a knock-on.

Suliasi Vunivalu also received a yellow card for a deliberate knock-on, gifting South Africa a second penalty try, and there was still time for Du Toit to go over from close range.

Australia barely managed to enter the South African half in a dismal second-half showing from former England head coach Jones' side, but Gordon ran clear late on to reduce the arrears.

"I'm really proud of the boys, it was a fantastic performance," South Africa captain Duane Vermeulen said.

"We played to our strengths. We can still improve, it was not 100% our best performance, but I'm very happy with the result."