While he has not been named in the team announced on Tuesday, coach Rassie Erasmus said it was possible that Etzebeth's twisted knee could recover and allow him to take his place in the side.
Erasmus was to discuss the matter after the side's Tuesday training session.
"He might have miraculously recovered, and the Doc said there is some science behind that, it's not just the will to play or the occasion."
In the meantime, Erasmus named loose forward Pieter-Steph du Toit to lock in Etzebeth's place.
Erasmus is in no doubt the All Blacks will come out with all guns blazing.
"They'll want to build winning momentum after bouncing back against Argentina following their disappointing opening game, and the rivalry between the Boks and All Blacks will motivate them even more.
"They'll still be hurting from the Rugby World Cup final, and they know how important a win will be to square things up and open up the Rugby Championship.
"They're a quality team with several players who have an X factor, and they constantly pose a threat to our defence, so we have to start well and be on the top of our game in all departments to try to build on what we have done in the competition so far.
"This will be a completely different challenge to that which Australia posed, and the next two Tests will require a proper step-up from us.
"But, we are excited to see if we can take our game to the next level and give ourselves the best chance to stake a claim for the Championship for the first time since 2019."
Erasmus said Etzebeth could have started if he was really needed, but they felt it was better to play someone who was fully fit.
"It's not ideal that we have so many injuries at lock, but we are pleased with how Ruan [Nortje] stood his man in our last match, and we are confident he'll combine well with Pieter-Steph at lock.
"This will serve as a fantastic opportunity for him to prove what he can do against one of the best teams in the world.
"It's also good to have a player of Jasper's [Wiese] 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, and we are looking forward to seeing his physicality combined with the rest of the back row."
Erasmus also gave his backline from the Springboks second Test against Australia in Perth a vote of confidence. Aphele Fassi will play his seventh Test at fullback ahead of Willie le Roux.
"Aphele made a strong statement against the Wallabies in Perth, so we are excited to see what they have to offer against a heavily attack-oriented All Blacks backline.
"We've seen what most of these players can do under pressure in Australia, and we're confident that they'll want to build on that against the All Blacks."
The South Africa team is: 1.Ox Nche (33), 2.Bongi Mbonambi (72), 3.Frans Malherbe (73), 4.Pieter-Steph du Toit (81), 5.Ruan Nortje (2), 6.Siya Kolisi (86), 7.Ben-Jason Dixon (3), 8.Jasper Wiese (27), 9.Cobus Reinach (34), 10.Sacha Feinberg-Mngomezulu (6), 11.Kurt-Lee Arendse (19), 12.Damian de Allenda (82), 13.Jesse Kriel (73), 14.Cheslin Kolbe (35), 15.Aphelele Fassi (6).
Substitutes: 16.Malcolm Marx (69), 17.Gerhard Steenekamp (4), 18.Vincent Koch (54), 19.Marco van Staden (22), 20.Elrigh Louw (6), 21.Kwagga Smith (45), 22.Grant Williams (13), 23.Handre Pollard (73).