Hooper will captain the Wallabies for a 60th time at Suncorp Stadium, surpassing the number of times George Gregan led Australia out.
A special occasion for the skipper will come six days after Quade Cooper marked his international return by kicking a dramatic winning penalty against the Boks on the Gold Coast.
Holder South Africa was consigned to a stunning 28-26 defeat in Queensland and trails leader New Zealand by five points.
Australia is unbeaten in six Tests against the Springboks on home soil ahead of the round-four showdown, after achieving their first win of this year's tournament last weekend.
The All Blacks have maximum points from three matches and can take another stride towards regaining the title by beating Argentina.