The two players have returned home from Australia after picking up injuries in the 32-25 victory over the Wallabies in Perth last weekend.
That triumph moved John Smit's world champions and Lions slayers nine points clear at the top of the Tri Nations table and puts them on the verge of reclaiming the title. They have now beaten the All Blacks and Wallabies twice and face the Aussies for a third time in Brisbane on Saturday.
Pietersen tore his hamstring late on in the game in Perth, while replacement lock Bekker suffered a grade 3 injury to the ACL joint in his shoulder. Neither player will be replaced.