The All Blacks outscored their hosts by four tries to three but the boot of new Springbok flyhalf Sacha Feinberg-Mngomezulu proved the difference as he contributed 16 points in the first meeting between the teams since October's Paris clash which South Africa won 12-11.
Bongi Mbonambi, Kwagga Smith and Grant Williams scored the home tries while Feinberg-Mngomezulu was successful with four penalties and two conversions.
Caleb Clarke ran in two tries and Codie Taylor and Jordie Barrett got one each for the visitors as Damian McKenzie added a penalty and two conversions.
It was a third victory in the southern hemisphere championship for South Africa, who were 27-17 down with 11 minutes left but used their forward power to snatch a late win.
"We made sure not to panic and picked ourselves up. We didn’t give up, we’ve been behind before and we can draw on those experiences,” said South Africa captain Siya Kolisi.
Yellow Card
The turning point proved the yellow card for Ofa Tu'ungafasi in the 68th minute and Smith scored after a sustained attack before Williams drove over for a 75th minute to secure the win.
The opening two tries both came from line-out mauls with New Zealand going over in the seventh minute after sustained pressure from the kickoff.
South Africa’s opening try from Mbonambi came in the 17th minute but television replays showed he lost control of the ball as he went over the line. Inexplicably, the refereeing team allowed it to stand.
The Boks took the lead when Feinberg-Mngomezulu, who has taken over as first-choice flyhalf from World Cup hero Handre Pollard, slotted over a penalty from inside his own half in the rarified air of the Highveld.
The All Blacks pounced on a home error to send Clarke over for a try in the 33rd minute and they extended their 12-11 halftime lead two minutes into the second half as Jordie Barrett intercepted to silence the capacity crowd.
The sides exchanged penalties to put All Blacks 22-17 ahead before then another impressive burst of line speed sent Clarke over again.
It looked all over for the home team but their forward power turned the screws on the All Blacks and secured a thrilling comeback.
South Africa host New Zealand again in Cape Town next Saturday.
