Going into the last 13 minutes with a 27-17 lead, the All Blacks lost replacement prop Ofa Tu'ungafasi to the sin-bin and saw Springboks replacements flanker Kwagga Smith and halfback Grant Williams score tries courtesy of their lineout maul.
The South African revival came when the All Blacks attacked but failed to secure the ball when Rieko Ioane was tackled on the left flank. South Africa grabbed the ball and let fullback Aphelele Fassi use his speed before kicking deep. While the ball bounced into touch, South Africa went to their maul in the All Blacks 22m area.
Under an earlier warning in their 22m area, the All Blacks couldn't afford a mistake, but it came with Tu'ungafasi's maul infringement, and South Africa got within three points after Smith's try.
That was hit home in the 74th minute when another penalty kick to the corner after replacement flanker Samipeni Finau was penalised for changing his bind in a maul. And from the maul, Williams secured the lead.
It was frustrating for the New Zealanders who looked to be in control of the game, building on outstanding leadership from captain and lock Scott Barrett, and hooker Codie Taylor, their first try scorer in the contest.
But 27 missed tackles to 17 by South Africa, 66 rucks lost to 85 and 14 penalties conceded to five, all counted against the All Blacks.
They enjoyed a 12-11 lead at halftime and had a considerable boost a minute into the second half.
Second five-eighths Jordie Barrett pulled off an intercept as South Africa ran the ball to extend the lead to eight points. Penalty goals were exchanged, and the home team lost wing Kurt-Lee Arendse. Having earlier brought on their bomb squad, South Africa was forced to play Handre Pollard at second five-eighths, with the backs outside moving out a space.
That resulted in Clarke scoring his second try. The All Blacks threw a long lineout, and while it was not tidy, they retained the ball, which was moved through the line to give Clarke clear space to score in the 51st minute.
But, the South Africans used their experience and confidence to grind New Zealand down, and the cost of indiscipline, mistakes, especially in kicking accuracy, and the inability of the All Blacks' bench to stem the tide compounded the situation.
Controversy came early with Springboks fullback Aphelele Fassi sin-binned in the sixth minute for not retiring after a tackle close to his line. The All Blacks used the maul for Taylor to score from the resulting lineout.
South Africa then kicked the restart out on the full, and from the midfield scrum, All Blacks halfback TJ Perenara landed a 50-20 kick into the 22m area. But from the resulting play, he was penalised (one of seven by the All Blacks to two by the Springboks in the first half), allowing South Africa to get into All Blacks territory,
The home team used their maul for hooker Bongi Mbonambi to score, although replays showed he looked to lose the ball in scoring. Then, kicker, the impressive first five-eighths Sacha Feinberg-Mngomezulu was timed out in his conversion attempt.
But in the 30th minute, he showed his ability and danger with a 60-metre penalty goal to give South Africa the lead.
It proved only temporary as flanker Ben-Jason Dixon lost the ball in a tackle, and Taylor charged away with the ball. From the ruck, first five-eighths Damian McKenzie held his pass, beat a defender, and fed prop Tyrell Lomax, who also timed his pass to fullback Beauden Barrett to create space out wide. Will Jordan was across from his wing to feed Clarke, who dominated the air on his side of the ground, in for a try in the 32nd minute.
New Zealand achieved a slight edge in possession in the first half, forcing South Africa to make 71 tackles to 50 by the All Blacks, but the momentum change in the second half was reflected in New Zealand having to make 127 tackles to 110.
Scorers: South Africa 31 (Bongi Mbonambi, Kwagga Smith, Grant Williams tries; Sacha Feinberg-Mngomezulu 2 con, 4 pen) New Zealand 27 (Codie Taylor, Caleb Clarke 2, Jordie Barrett tries; Damian McKenzie 2 con, pen). HT: 11-12