Habana had been named in the team to play Scotland on Saturday but suffered the injury in his left hand when he fell awkwardly during morning practice.
His place in Saturday’s team is taken by uncapped Lwazi Mvovo — who is promoted from the bench — while the experienced Adi Jacobs joins the replacements.
Coach Peter de Villiers had already planned three changes when he promoted Zane Kirchner, Francois Hougaard and Ryan Kankowski to the starting team. In a further positional switch from the team who beat Wales 29-25 last weekend, Gio Aplon moves from fullback to wing in place of Bjorn Basson, who has gone home following injury and his provisional doping suspension.
With Chiliboy Ralepelle also out of the squad following his positive test for banned stimulant methylhexaneamine, hooker Adriaan Strauss comes on to the bench. Kirchner will start at full-back, Hougaard takes the number nine shirt after a good display off the bench against Wales, while Kankowski packs down at number eight.
De Villiers, who is concerned that the whole squad may have been exposed to methylhexaneamine via their energy drinks or products, said that the players had got over the shock of the positive tests.
“We have moved on, we’re professional, we know how to deal with tough moments and we look forward to playing the game on Saturday,” said De Villiers.
The Springboks have scaled back their use of nutritional supplements and sent them for analysis.
“We have sent a lot of stuff for testing. We don’t want to repeat it.”
Meanwhile, Flanker Ryan Jones will captain a Wales team against Fiji on Friday showing a probable nine changes from the starting XV beaten by South Africa last weekend. The changes include a first test start in three years for Aled Brew, who replaces winger Shane Williams after he dislocated his shoulder in the 29-25 defeat by the world champions in Cardiff. Flanker Dan Lydiate is also included, as long as he overcomes an ankle problem, to replace Martyn Williams. Teenage wing George North, who scored two tries on his debut against the Springboks, retains his place while uncapped 20-year old Tonga-born flanker Toby Faletau is included among an otherwise experienced-looking group of replacements.
SOUTH AFRICA (v Scotland): Z Kirchner; G Aplon, F Steyn, J de Villiers, L Mvovo; M Steyn, F Hougaard; T Mtawarira, B du Plessis, J du Plessis, B Botha, V Matfield (capt), D Stegmann, J Smith, R Kankowski.
Replacements: A Strauss, CJ van der Linde, F van der Merwe, W Alberts, R Pienaar, P Lambie, A Jacobs.
WALES (v Fiji): L Byrne; G North, J Hook, A Bishop, A Brew; D Biggar, R Rees; P James, H Bennett, A Jones, I Gough, D Jones, R Jones (capt), D Lydiate/M Williams, J Thomas.
Replacements: R Hibbard, J Yapp, B Davies, T Faletau, M Phillips, S Jones, T Shanklin.
FRANCE (v Argentina): A Palisson, Y Huget, A Rougerie, Y Jauzion, M Andreu, D Traille, M Parra, T Domingo, W Servat, N Mas, J Pierre, L Nallet, T Dusautoir, J Bonnaire, S Chabal.
Replacements: G Guirado, L Ducalcon, J Thion, I Harinordoquy, D Yachvili, F Estebanez, J Porical.