Proteas test captain Hashim Amla says the player has been struggling with a hamstring injury.
South Africa sailed into the semi-finals with a three-run victory over former champions England.
Proteas Test captain Graeme Smith will retire after the current Test series against Australia.
The Aussies were set 448 for victory after Graeme Smith declared on 270 for 5 before lunch.
Hashim Amla finished the third day within seven runs of his 21st Test century.
AB de Villiers has praised his team’s performance but admits there are things they need to work on.