The 32-year-old Nortje pulled up in his fourth over and played no further part in the test, which South Africa won by an innings and 31 runs on Thursday.
His absence is the only change to the squad for the third test, which starts at Newlands on Tuesday.
Nortje had only returned after a lengthy spell out of first-class cricket after a litany of injuries stalled his career.
South Africa and Australia are level at 1-1 in the three-match series after the tourists won the firest test by 214 runs in Durban and the home side responded with an innings victory in Gqeberha.
South Africa Squad:
Temba Bavuma (captain), Marques Ackerman, David Bedingham, Corbin Bosch, Matthew Breetzke, Gerald Coetzee, Simon Harmer, Marco Jansen, Keshav Maharaj, Aiden Markram, Wiaan Mulder, Senuran Muthusamy, Dane Paterson, Kagiso Rabada, Ryan Rickelton, Kyle Verreynne.