As expected, most players sent as an advance guard have been included in the side.
Coach Jacques Nienaber said the selection was based on striking a balance between the players who beat Australia and those sent ahead to adjust to the time zone differences.
Only five players have been retained to play the All Blacks, fullback Willie le Roux, centre Lukhanyo Am, props Steven Kitshoff and Frans Malherbe, and hooker Bongi Mbonambi.
He said the selectors had stuck to a deliberate plan.
"I am not going to say if there were guys who played their way in. We have been open with the players from the start as to who would start against Australia and who against New Zealand.
"We always wanted that blend, and that is why we, more or less, had two squads.
"The guys who went early to New Zealand first spent a lot of time in Pretoria helping prepare the team for Australia, and now all the guys who have come over later will prepare this team for the All Blacks.
"As these guys are sitting here, their bodies are fresh and better adjusted, but they haven't had international rugby exposure this year. The other guys are a bit stiff and sore, but they have a proper Test match under their belt."
Nienaber said they needed to employ a squad system to be competitive enough in the Championship to give them a chance to win. They would also need a squad for their two warm-up Rugby World Cup games against the Welsh and the All Blacks.
"There was never an A and B squad for these first two games. We felt the team for Loftus Versfeld was the right mix for Australia and for the All Blacks we picked a team that will give us the best chance of beating a different kind of team."
In the loose, they have gone for Kwagga Smith on the openside flank, Franco Mostert on the blindside and Jasper Wiese at No8.
"They might not have played together much in this combination but each has experience in his position."
The team is: 1.Steven Kitshoff, 2.Bongi Mbonambi, 3.Frans Malherbe, 4.Eben Etzebeth (captain), 5.Lood de Jager, 6.Kwagga Smith, 7.Franco Mostert, 8.Jasper Wiese, 9.Faf de Klerk, 10.Damian Willemse, 11.Makazole Mapimpi, 12.Damian de Allende, 13.Lukhano Am, 14.Cheslin Kolbe, 15.Willie le Roux.
Substitutes: 16.Malcolm Marx, 17.Thomas du Toit, 18.Vincent Koch, 19.RG Snyman, 20.Pieter-Steph du Toit, 21.Duane Vermeulen, 22.Grant Williams, 23.Manie Libbok.