Nortje broke down midway through his fourth over in the first innings of the second Test at St George's Park, which the Proteas still went on to win to level the series despite being a bowler down.
It was always a big ask for Nortje to play back-to-back Test matches, with the opening game of the series in Durban the paceman's first long format game in three years and sending down 40 overs.
The hosts have opted not call on a replacement as they feel they have sufficient depth in the squad of 16 players already in camp in Cape Town.
Corbin Bosch or Gerald Coetzee would be favourite to come into the Proteas XI as they are the quickest of the fast bowling reserves, while seamer Dane Paterson could also be in contention to offer more control.
The Proteas could also change the dynamic of their attack and replace Nortje with a spinner as Keshav Maharaj and Senuran Muthusamy wait for an opportunity, which is unlikely.
Australia won the opening Test in Durban by 214 runs before the Proteas bounced back emphatically to beat the tourists by an innings and 31 runs in Gqeberha.
Simon Harmer hailed the Proteas' ability to bounce back in the second Test against Australia and says they will be looking to "put our best foot forward" in the series decider at Newlands.
South Africa produced a dominant performance to beat Australia by an innings and 31 runs in the second Test at St George's Park in Gqeberha on Thursday, levelling the series at 1-1.
South Africa produced a commanding performance to defeat Australia by an innings and 31 runs in the second Test at St George's Park in Gqeberha, with captain Temba Bavuma leading the way with a magnificent 179.
Marco Jansen took a five-wicket haul as the Proteas skittled Australia out for just 99, before the tourists found themselves in trouble following-on at 156-4, still trailing by 170 runs.
