Injury rules out loose forward Ethan Blackadder (hamstring) and winger Caleb Clarke (back), who scored two tries in their 31-27 loss to the Springboks in Johannesburg last weekend.
Will Jordan shifts to fullback, Sevu Reece comes in on the right wing with Mark Tele'a brought in on the left with Clarke ruled out of Saturday's clash.
Perenara is replaced at scrumhalf by Cortez Ratima, who gets only his second start for the All Blacks while Wallace Sititi, who made his debut in July, takes the place of Blackadder on the blindside of the scrum.
Flanker Luke Jacobson is preferred to Samipeni Finau among the replacements, as New Zealand retain a 5-3 split between forwards and backs on the bench.
Meanwhile, Springboks coach Rassie Erasmus has made seven changes, including two positional switches, to his winning line-up.
Winger Canan Moodie and scrumhalf Hendrikse have been named to make their first appearances since the World Cup, Hendrikse from the bench. Moodie replaces Kurt-Lee Arendse who has a concussion, and Cheslin Kolbe moves from the right wing to the left.
Two-time World Cup winners Willie le Roux and Lukhanyo Am also return to the side, le Roux at fullback and Am on the bench.
Lock Eben Etzebeth returns to the starting line-up after being named among the reserves in the first Test due to a knee injury. Pieter-Steph du Toit, who started in the second row in place of Etzebeth, returns to his usual place at flanker.
Scrumhalf Grant Williams will also start for the first time this season after scoring the match-winning try last weekend as a replacement, while Handre Pollard takes over from Sacha Feinberg-Mngomezulu at flyhalf.
Captain Siya Kolisi has been passed fit after suffering a heavy head knock in Johannesburg.
"This match is going to massive," Erasmus said. "New Zealand are a world-class outfit and we know that they'll be desperate to bounce back after leading in the second half last week."
STARTING LINE-UPS
New Zealand: Will Jordan, Sevu Reece, Rieko Ioane, Jordie Barrett, Mark Tele'a, Damian McKenzie, Cortez Ratima; Ardie Savea, Sam Cane, Wallace Sititi, Tupou Vaa'i, Scott Barrett (captain), Tyrel Lomax, Codie Taylor, Tamaiti Williams. Reserves: Asafo Aumua, Ofa Tu'ungafasi, Fletcher Newell, Sam Darry, Luke Jacobson, T.J. Perenara, Anton Lienert-Brown, Beauden Barrett
South Africa: Wille le Roux, Canan Moodie, Jesse Kriel, Damian de Allende, Cheslin Kolbe, Handre Pollard, Grant Williams; Jasper Wiese, Pieter-Steph du Toit, Siya Kolisi (captain), Ruan Nortje, Eben Etzebeth, Frans Malherbe, Bonbi Mbonambi, Os Niche. Reserves: Malcolm Marx, Gerhard Steenekamp, Vincent Koch, Kwagga Smith, Elrigh Louw, Jaden Hendrikse, Sacha Feinberg-Mngomezulu, Lukhanyo Am
