Adriaan Strauss will start at hooker and Morné Steyn at flyhalf when the Springboks meet the Wallabies in Perth on Saturday.
Bismarck du Plessis moves to the bench, with Handré Pollard dropping out of the 23-man squad.
In other changes to the team that beat the Pumas 33-31 in Salta, Jan Serfontein starts at outside centre with Marcell Coetzee, Victor Matfield, Adriaan Strauss and Tendai Mtawarira included in the pack.
Lood de Jager and Damian de Allende shift to the bench, and are joined there by Trevor Nyakane, Marcel van der Merwe, Pat Lambie and the uncapped Warren Whiteley.
'We were always planning in moving our personnel around during the competition,' said Bok coach Heyneke Meyer. 'The only new player in the team is Warren, whom I’m very happy for and excited to see what he can do. He covers all three positions in the loose trio and can make an impact later in the game.
'It’s also good to see Pat back in the frame. He’s completed his comeback from a long-term injury and will provide necessary bench cover for flyhalf and fullback.
'Saturday’s Test against Australia will take a massive effort from every member of our squad. We’re not looking at their recent result against New Zealand and we know they will be a tough opponent.
'Similarly, we need to move on from our victories over Argentina, which are now in the past. This is a new challenge and one we have to overcome to stay alive in the competition.'
Meanwhile, Bryan Habana will on Saturday become the fourth Springbok and 33rd player overall to play in 100 Tests.
The 31-year-old, who made his debut for South Africa against England at Twickenham on 20 November 2004, holds the record for the most Test tries in a Springbok jersey. His 56 Test tries places him fourth on the list of all-time international try-scorers.
The three-time South African Rugby Player of the Year (2004, 2007 and 2012), who was also named the IRB Player of the Year in 2007, will lead the Springboks out on Saturday as he follows Percy Montgomery, John Smit and Victor Matfield in amassing 100 Tests in the green and gold.
'This is an unbelievable achievement by Bryan, who is someone every South African can be immensely proud of,' said Meyer. 'Bryan is a true professional and someone who never gives anything but his best, on the field and off it. For him to reach this magnificent milestone is just reward for years of dedication and hard work.
'Apart from scoring tries and always giving 100% on the field, Bryan is also a humble servant to the game and a true ambassador for his family, his friends and his country. He will go down in history as one of the greatest rugby players of all time.
'He is always looking for improvement – I’ve never seen him play a bad game in the Springbok jersey.'
Springboks – 15 Willie le Roux, 14 Cornal Hendricks, 13 Jan Serfontein, 12 Jean de Villiers (c), 11 Bryan Habana, 10 Morné Steyn, 9 Ruan Pienaar, 8 Duane Vermeulen, 7 Marcell Coetzee, 6 Francois Louw, 5 Victor Matfield, 4 Eben Etzebeth, 3 Jannie du Plessis, 2 Adriaan Strauss, 1 Tendai Mtawarira.
Subs: 16 Bismarck du Plessis, 17 Trevor Nyakane, 18 Marcel van der Merwe, 19 Lood de Jager, 20 Warren Whiteley, 21 Francois Hougaard, 22 Pat Lambie, 23 Damian de Allende.
Photo: Daniel Jayo/Getty Images