Habana has failed a late fitness test on a hamstring injury, having missed last weekend's defeat to Australia.
The Springboks, who will hope to arrest a run of three straight defeats, are also without Francois Steyn, who has concussion, and JP Pietersen (hamstring).
However, coach Peter de Villiers is boosted by the availability of Victor Matfield and Bismarck du Plessis, who were both doubtful with groin and knee problems respectively.
Prop CJ van der Linde misses out as he has been suspended for four weeks for headbutting Australia's Sam Cordingley last weekend.
South Africa team: Conrad Jantjes, Odwa Ndungane, Adrian Jacobs, Jean de Villiers, Jongi Nokwe, Butch James, Fourie du Preez; Tendai Mtawarira, Bismarck du Plessis, Brian Mujati, Andries Bekker, Victor Matfield, Schalk Burger, Juan Smith, Pierre Spies.
Replacements: Adriaan Strauss, Jani du Plessis, Danie Rossouw, Luke Watson, Ricky Januarie, Ruan Pienaar, Percy Montgomerie.