Again, it was the super sub hooker Malcolm Marx who punished All Blacks' indiscipline which saw prop Tyrel Lomax mar an otherwise fine performance by a late charge on Springbok wing Cheslin Kolbe as he attempted to follow through a kick to the All Blacks' line.
From the resulting penalty kick to the corner, real estate South Africa used to pressure the New Zealanders throughout the second half. The maul was played, and Marx went blindside to score in the corner to go out to an 18-12 lead that the All Blacks could not pull back.
The win all but sealed the Championship for South Africa, saw them claim the Freedom Cup for the first time since 2009 and completed four consecutive wins over the All Blacks for the first time since 1949.
Tryless, the All Blacks saw Springboks skipper Siya Kolisi score eight minutes into the second half, to give his side an advantage and a hold on the game the All Blacks couldn't slip.
It was a game of dynamic defence, some powerful tackles being applied, and while South Africa missed 37 tackles to only 20 by New Zealand, the desperation of the home side and the seeming impatience of the All Blacks the further into the game they went, minimised their chance to pull the game from the fire.
All Blacks' first five-eighths, Damian McKenzie, missed two penalty goal attempts, and while the first hit the post and was reclaimed by second five-eighth Jordie Barrett, the All Blacks couldn't cash in on the chance.
Their best chance of the half faltered when skipper and lock Scott Barrett couldn't hold a ball that hit him in the face as a promising move shaped. This summed up the side's continuing inability to complete opportunities.
South Africa, down 3-9 at halftime, came out and looked to move the ball around more. Once in the All Blacks' 22m area, they poured on the pressure. Three penalties were awarded, and the Springboks got into the corner and pounded the defence.
Eventually, after eight minutes from a lineout, captain and flanker Siya Kolisi crossed for the game's first try.
The second half contrasted with a more controlled display in the first 40 minutes.
Days of All Blacks-Springboks past were played out with thrust typically met by counter-thrust. It was bruising as both sides got their power play working.
South Africa twice got close to the All Blacks' line, but superb tackling dropped the big men quickly, with flanker Sam Cane, captain and lock Barrett, prop Lomax and outstanding hooker Codie Taylor all making crucial plays. The pressure was on the home side as they coughed up the ball, and Cane, Barrett, and halfback Cortez Ratima picked off the turnover ball.
The All Blacks looked to get their running game going, and on the few occasions they could, they looked likely to have Taylor again leading the way with solid runs with the ball in hand. He had good support from new blindside operator Wallace Sititi, who stepped into the white-hot atmosphere with relish.
They proved capable of opening up gaps the more they moved and retained the ball and saw South Africa miss 26 tackles to seven, but the difference came when South Africa denied them the continuity they sought.
That involved conceding penalties in their 22m area, and McKenzie took the chance to land two penalty goals from close to the posts, adding another from 42 metres for a halftime lead of 9-3.
The challenge doesn't ease as the All Blacks attempt to retain the Bledisloe Cup in their final two games of the Championship against a resurgent Australian team.
Scorers: South Africa 18 (Siya Kolisi, Malcolm Marx tries; Handre Pollard con, pen; Sacha Feinberg-Mngomezulu pen) New Zealand 12 (Damian McKenzie 4 pen). HT: 3-9