Having made a duck on his ODI debut, Janneman Malan struck an unbeaten 129 on Wednesday to steer South Africa to victory in Bloemfontein.
Temba Bavuma will play no further part in the ODI series against Australia, but will fly out to face India this weekend.
South Africa have brought back Faf du Plessis and Rassie van der Dussen for the three-match ODI series with India.
Heinrich Klaasen's unbeaten century laid the foundations for South Africa to beat Australia in the first of three ODIs on home soil.
South Africa have announced Kagiso Rabada suffered a groin strain during the Twenty20 series against Australia on home soil.
South Africa managed just 96 in reply to Australia's total of 193-5 as the tourists dominated the series decider in Cape Town.
Keshav Maharaj is back in the ODI fold for South Africa, but Faf du Plessis will sit out again against Australia.
Jhye Richardson will remain in South Africa after Australia announced their squad for a series against New Zealand from March 13-20.
South Africa levelled the Twenty20 series against Australia at 1-1 thanks to some excellent bowling in the closing overs.
South Africa were skittled for 89 by Australia at the Wanderers, as leg-spinner Ashton Agar took five wickets including a hat-trick.