The world champions have six locks ruled out, including Eben Etzebeth (foot), requiring a move from flanker to the second row for Du Toit and a third international cap for Nortje.
"It's not ideal that we have so many injuries, but we are pleased with the way Ruan stood (up) in our last match and we are confident he will combine well with Pieter-Steph," coach Rassie Erasmus told reporters on Tuesday.
"Eben may have been ready to play this week if we really needed him, but we feel we will benefit more from selecting a player that is 100 per cent fit."
Better news for Erasmus is the return from a six-game suspension of No.8 Jasper Wiese and he will be in the back row of the scrum with flankers Ben-Jason Dixon and captain Siya Kolisi.
"It's also good to have a player of Jasper's calibre back and we know that he'll bring a lot of energy on attack and defence after biding his time to return to the field. We are looking forward to seeing his physicality combined with the rest of the back row," Erasmus said.
Bongi Mbonambi is at hooker, with props Ox Nche and Frans Malherbe either side of him.
Sacha Feinberg-Mngomezulu gets the nod at flyhalf ahead of the more experienced Handre Pollard and Cobus Reinach will wear the No.9 jersey.
South Africa lead the Rugby Championship table after two rounds following a full haul of 10 points from bonus-point wins in Australia.
New Zealand are second with five points. The second meeting between the sides will be in Cape Town on September 7.
Team: Aphelele Fassi, Cheslin Kolbe, Jesse Kriel, Damian de Allende, Kurt-Lee Arendse, Sacha Feinberg-Mngomezulu, Cobus Reinach, Jasper Wiese, Ben-Jason Dixon, Siya Kolisi (capt), Ruan Nortje, Pieter-Steph du Toit, Frans Malherbe, Bongi Mbonambi, Ox Nche. Replacements: Malcolm Marx, Gerhard Steenekamp, Vincent Koch, Marco van Staden, Elrigh Louw, Kwagga Smith, Grant Williams, Handre Pollard.
