The world champion Springboks were much improved on their sloppy showing in the first test and had the ascendency in the contact area and breakdown in another bruising battle.
Centres Jesse Kriel and Damian de Allende also scored tries to go with 18 points from the boot of wing Cheslin Kolbe to the delight of most of the 56,589 in attendance.
New Zealand scored four tries through scrumhalf Cam Roigard, fullback Damian McKenzie, wing Leroy Carter and number eight Ardie Savea, but were disrupted at the line-out and have some work to do at the set-piece ahead of the third match in Johannesburg on Saturday.
"It has been a tough week, but I am grateful for the coaching staff and the plans they made for us. Last week we did not take our opportunities and this week we did," Kolisi said. "Next week will be big too. It is hard playing them once, but four times is very difficult."
Savea rued some inaccuracy from his side and allowing South Africa to get away early in the game.
"It is unfortunate," he said. "You cannot let the Springboks get ahead like that and we were chasing the game. I am proud of the boys we stuck in there but came up short. It is a tough pill to swallow.
"In accuracy and discipline, that punished us today. We need to sort that out. We lost the battle tonight but not the war."
The Springboks showed their power and much more precision than last week from the start as they mauled a line-out for 20-yards before moving the ball down the backline for Kriel to score.
The All Blacks had a concerted period of pressure in the Springbok half after that and but were repelled until Will Jordan slipped a couple of tackles on the right wing and set Roigard free to score.
The hosts were wasteful with their entries into the New Zealand 22 last week, but were more clinical this time round as De Allende stretched to score after a strong run from flyhalf Sacha Feinberg-Mngomezulu.
New Zealand looked dangerous every time they had ball in hand though and were finding gaps in some porous home defence, allowing McKenzie to cross in the corner.
The seesaw contest continued as the Springboks scored next when captain Kolisi burrowed over on his return to the side from injury as the hosts led 24-14 at the break.
Kolbe landed two penalties early in the second period to extend the Springbok lead to 16 points.
The visitors toiled to break down the home defence in the second half, but stayed in the game when Carter crossed in the corner and Savea went over from close range, before another Kolbe penalty.
South Africa finished the game with 14 players following a yellow card for Lood de Jager but held on for the win.