After being sent in to bat in the opening encounter of the five-match series, the home team posted 300 for eight from their 50 overs.
In reply, South Africa threatened a record run chase at the venue when their skipper, AB de Villiers (80) and David Miller (65) put on 126 for the fifth wicket, but ultimately fell 32 runs short and were dismissed for 268.
Despite the efforts of de Villers and Miller, the South Africans were always on the back foot after losing early wickets, with paceman Mitchell Johnson (2-38) celebrating his announcement as the ICC Cricketer of the Year by claiming both Proteas openers, Quinton de Kock and Hashim Amla, in quick succession.
The 33-year-old Clarke reinjured his troublesome left hamstring as he made just 11 from 20 balls in the Australian innings and was immediately ruled out of taking any further part in the match.
Also Read
Clarke has battled a degenerative back condition in recent years and hamstring troubles have plagued him, including missing matches on Australia's past two overseas tours, to Zimbabwe and the United Arab Emirates.
The injury will be assessed on Saturday and Clarke conceded it was a major concern for his playing future.
"I've had a long stint of rehab trying to get it strong and unfortunately it's come back again, so that is not positive.
"But I know I've got experts looking at it, I'm in good hands, and I will just have to listen to them.
"I think we're in for a great summer. I just hope I can be a part of it.