Barrett fell heavily on his neck during last weekend's opening 26-10 loss to the Springboks and although he has trained this week, he will start from the bench.
That defeat was the All Blacks' heaviest to the Boks in 94 years and continued a spate of losses that have dropped New Zealand to No.5 in the world rankings and cast major doubt on the future of coach Ian Foster beyond this weekend.
Other changes are in the forward pack, where the visitors were dominated in the first clash, with Shannon Frizell coming in at flanker to replace Akira Ioane, who drops to the bench, and props Tyrel Lomax and Ethan de Groot in for Angus Ta'avao and George Bower respectively.
Uncapped tighthead prop Fletcher Newell will start among the replacements.
"Belief and confidence remain high in our group, which is working incredibly hard this week," Foster said in a media release from New Zealand Rugby.
"Playing at Ellis Park is always a special occasion for any All Black team, and this weekend will be no different."
This could well be his last selection as head coach if the team lose, though even victory may not be enough to keep him in the post after the side lost five of their previous six Tests and the tide of public opinion is very much against Foster back home.
Fullback Jordie Barrett and wing Will Jordan had been doubts for the game but have been passed fit and will make up a back three with Caleb Clarke.
David Havili and Rieko Ioane continue their partnership in the centres, with Aaron Smith at scrumhalf alongside Mo'unga.
Frizell is joined in the back row of the scrum by Ardie Savea and captain Sam Cane, Scott Barrett and Sam Whitelock are the lock pairing, and Samisoni Taukei'aho continues at hooker with the two new props alongside him.
New Zealand: 15-Jordie Barrett, 14-Will Jordan, 13-Rieko Ioane, 12-David Havili, 11-Caleb Clarke, 10-Richie Mo'unga, 9-Aaron Smith, 8-Ardie Savea, 7-Sam Cane (captain), 6-Shannon Frizell, 5-Scott Barrett, 4-Sam Whitelock, 3-Tyrel Lomax, 2-Samisoni Taukei'aho, 1-Ethan de Groot. Replacements: 16-Codie Taylor, 17-George Bower, 18-Fletcher Newell, 19-Tupou Vaa'i, 20-Akira Ioane, 21-Finlay Christie, 22-Beauden Barrett, 23-Quinn Tupaea.
