The world champion Springboks were determined to respond after they were stunned in the first test in Johannesburg last week.
Skipper Siya Kolisi marked his return from injury with a try as the hosts were much improved on their sloppy showing in the first test and had the ascendancy 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.
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.
Kolisi said the Boks last week paid the price for not taking their chances, but said: "This week we did, and we also brought the fire."
The scrum was the decisive battleground in the first test in Johannesburg and Springboks coach Rassie Erasmus tried to fix that by swapping his entire front rows at the last minute.
Hooker Deon Fourie didn't have to wait to become the oldest Springbok test player a month before his 40th birthday.
New Zealand's scrum generally held firm but it was the lineouts where the All Blacks malfunctioned at critical moments.
Three attacking throw-ins by the All Blacks were spoiled by Eben Etzebeth, who made one steal. South Africa's first two tries were platformed by lineout mauls.
"South Africa were good tonight, really physical. They stopped a lot of our momentum," New Zealand coach Dave Rennie told SuperSport.
"We're confident we can bounce back."
The All Blacks came into the match perfect under new coach Rennie after wins in four tests and four matches against South African franchises.
The return to Johannesburg for the third test next Saturday at 87,000-seat Soccer City.
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