Moving Kolisi means flanker Marco van Staden comes into the starting lineup with reigning World Rugby Player of the Year Pieter-Steph du Toit completing the back row.
Manie Libbok gets the nod at first five-eighths before Handre Pollard and Sacha Feinberg-Mngomezulu, with head coach Rassie Erasmus well aware of the record of the Japan-based playmaker.
The Springboks have lost only one of 13 tests when Libbok has started – the pool defeat by Ireland at the 2023 World Cup in France.
But when the 28-year-old came off the bench in seven internationals, record four-time World Cup winners South Africa lost four.
Creative Libbok is capable of opening the tightest defences, but doubts remain over his goal kicking, a skill perfected by Pollard.
Grant Williams has moved to the front of the queue for the hotly contested halfback position and starts with veteran Cobus Reinach providing cover on the bench.
Erasmus has opted not to risk star wing Cheslin Kolbe or veteran centre Damian de Allende as both are recovering from niggles.
Edwill van der Merwe, who has scored five tries in three tests, replaces Kolbe on the right wing while Andre Esterhuizen fills in for De Allende at second five-eighths.
“Cheslin has recovered from a niggle and trained with us last week, but we decided to exercise caution and give him extra time at training before selecting him,” said Erasmus.
“Damian picked up a back niggle and will train this week, but Andre has been strong for us in the last few seasons, so it was an easy decision to name him alongside Jesse [Kriel].”
Australia flew to Johannesburg after a 2-1 series loss to the British and Irish Lions. The Wallabies want to snap a four-match losing streak against South Africa and will name their team on Thursday.
Springboks team to play Australia
15 Aphelele Fassi; 14 Edwill van der Merwe, 13 Jesse Kriel, 12 Andre Esterhuizen, 11 Kurt-Lee Arendse; 10 Manie Libbok, 9 Grant Williams; 8 Siya Kolisi (capt), 7 Pieter-Steph du Toit, 6 Marco van Staden; 5 Lood de Jager, 4 Eben Etzebeth; 3 Wilco Louw, 2 Malcolm Marx, 1 Ox Nche
Replacements: 16 Bongi Mbonambi, 17 Jan-Hendrik Wessels, 18 Asenathi Ntlabakanye, 19 Franco Mostert, 20 Kwagga Smith, 21 Cobus Reinach, 22 Canan Moodie, 23 Damian Willemse