Zane Kirchner and Pat Lambie are both doubtful for Saturday's clash in Port Elizabeth after suffering injuries in the first two Tests.
The Springboks already know they must make at least one change in the back line with centre Frans Steyn unavailable because he is due to get married.
Pietersen himself has only just returned to training after a back injury.
Springboks coach Heyneke Meyer said: "Joe has always been part of our plans and also attended our final planning camp in Durban shortly before the England series started.
"Injuries are part of the game and something you can't plan for, but we always knew Frans was not going to be available for this Test.
"Joe knows our systems and game plans and I'm sure he will slot in easily."
Lambie has undergone a scan after sustaining an ankle injury in Saturday's second Test victory in Johannesburg. He will be reassessed later in the week along with Kirchner, who injured a knee in the first Test.
Flanker Willem Alberts is also doubtful with a knee injury and a decision will be made by Wednesday, when Meyer is due to name his team.
Meyer said: "We've decided not to call up a replacement for Willem as we have enough cover amongst the loose forwards in the squad."
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