The All Blacks' unbeaten streak is over after a late Pat Lambie penalty handed the Springboks a momentous 27-25 win in Johannesburg.
A thrilling Test mirrored the intensity of last year's memorable encounter at Ellis Park, but not the result, as reserve first five-eighth Pat Lambie kept his nerve in the 78th minute, landing a 54m penalty goal.
It ended a five-Test losing streak against the All Blacks for South Africa and also stopped the world champions' unbeaten run of 22 Tests.
It was also the All Blacks first Test loss in the Rugby Championship since the competition expanded to four nations but not enough to prevent them from winning the title, which was clinched with a round to spare.
Both teams scored three tries, with the All Blacks launching a late assault after trailing 21-13 at halftime.
They looked to have snatched a late win when tries to wing Ben Smith and hooker Dane Coles put them 25-24 ahead.
However, a high tackle from reserve flanker Liam Messam on Schalk Burger gave away the penalty that proved decisive.
The All Blacks launched another late assault but were denied when losing ruck turnover ball to Springboks No.8 Duane Vermeulen, who produced a heroic 80 minutes after being cleared late to start despite a rib injury.
His act typified the Springboks' approach to the breakdown, where their aggression forced the All Blacks into multiple turnovers, particularly in the first half.
First five-eighth Handre Pollard made them pay with a 19-point haul, including two tries.
The 20-year-old was at the sharp end of an impressive backline, which was determined to keep the ball hand and helped the hosts dominate the first half statistics.
Springboks captain Jean de Villiers talked up the importance of toppling the All Blacks a year out from the World Cup.
"It's definitely one of the boxes we wanted to tick before next year," he said.
"I must give credit to this New Zealand team, they were unbelievable in that second half. They almost took it away from us."
Counterpart Richie McCaw rued an error-ridden start: "It was a pretty tough old first half but we kept believing and we gave ourselves a chance.
"There wasn't much in it at the end and I'm hugely proud of the boys but it's still disappointing to come second."
Pollard began inauspiciously by missing a kickable penalty before opposite Beauden Barrett slotted one of his own.
South Africa opened their account with a brilliant 80m try to halfback Francois Hougaard, started by fullback Willie le Roux from a turnover.
Barrett's second penalty was again trumped by a Springboks try, when Pollard sliced through a clump of All Blacks tight forwards to cross untouched.
Second five-eighth Malakai Fekitoa reduced the margin to one with his first Test try, started 70m out through a classy chip and chase from wing Julian Savea.
However, Pollard bagged his second try soon after halftime, twisting over in the tackle of McCaw.
A Pollard penalty extended the lead to 24-13 before momentum swung.
A clean bust from centre Conrad Smith created the overlap for wing Ben Smith before quick hands from a number of All Blacks forwards sent hooker Dane Coles across four minutes later for his first try in 23 Tests.
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