And there is also no place in the Springboks 22 for prop Tendai Mtawarira in a side that will be captained by hooker John Smit.
A Springboks press release revealed Botha, who missed early games in the tournament due to his injury, was hurt again during training on Tuesday.
At this stage, he is not being sent home, with the Springboks management set to reassess his situation on Monday. Danie Rossouw and Victor Matfield will forge the second-row partnership this weekend.
Gurthro Steenkamp is preferred to Mtawarira, packing down alongside Smit and Jannie du Plessis, while centre Jean de Villiers returns as replacement for Frans Steyn, who exited the World Cup last weekend because of a shoulder injury.
And wings Bryan Habana and J P Pietersen have both allayed any fears about their fitness by both being named in the starting line-up.
The Springboks side is the most experienced in their Test match history, containing a total of 836 caps to surpass a previous record of 815 set against opening Pool D opponents Wales in Wellington last month.
The team includes eight players who started the 2007 World Cup final against England in Paris, plus three players who were part of that squad.
South Africa are bidding to become the first team to successfully defend the World Cup, with victory on Sunday meaning they will play New Zealand or Argentina in the semi-finals.
Team: P Lambie; J P Pietersen, J Fourie, J de Villiers, B Habana; M Steyn, F du Preez; G Steenkamp, J Smit (capt), J du Plessis, D Rossouw, V Matfield, H Brussow, S Burger, P Spies.
Replacements: B du Plessis, C J van der Linde, W Alberts, F Louw, F Hougaard, B James, G Aplon.
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