The All Blacks have lost four matches in a row against South Africa for the first time since 1949 after an 18-12 defeat in Cape Town.
The All Blacks were strong for most of the game but once again failed to score in the last 20 minutes of the game to close out the match.
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In a tense and high-energy match played in front of a crowd of 55,000, both sides made numerous errors as they tried their hand to score.
Springboks captain Siya Kolisi, playing with a fractured nose, crossed early in the second half and Malcolm Marx late on as the world champions edged the arm-wrestle and took a giant step towards the Rugby Championship title.
Flyhalf Damian McKenzie kicked all of New Zealand's points but missed two penalties from close in front that proved decisive for the visitors, who have now lost three of their last four tests in a difficult start for new coach Scott Robertson.
However ,it should be noted that McKenzie otherwise had a good test as did the majority of the forward pack, especially Codie Taylor and relative newcomer Wallace Sititi.
New Zealand were dominant at the breakdown, which kept them in the game as they won a succession of penalties.
But once again they battled to contain the home side in the final 20 minutes as the Springboks began to dictate territory and possession, and turned the screw on their visitors.
The All Blacks led 9-3 at halftime after both sides put in strong defense, with a yellow card each for Springbok number eight Jasper Wiese and All Black wing Sevu Reece.
South Africa found some power off the bench early in the second half and led for the first time in the game on 49 minutes after they camped in the New Zealand 22 and Kolisi went over from close range.
They traded penalties before the Springboks were down to 14 players again when fullback Willie le Roux knocked the ball on as he attempted an intercept.
McKenzie should have put New Zealand ahead with eight minutes remaining but missed a penalty from in front of the posts and the visitors were also reduced to 14 players for the second time after Tyrel Lomax's blatant obstruction of Cheslin Kolbe.
From the resulting attacking lineout, Marx crossed for the home side's second try as he burst free from the maul to dive over in the corner.
South Africa have 18 points at the head of the Rugby Championship table, followed by New Zealand with seven, who now cannot catch them with two games against Australia remaining.
Argentina (five points) and Australia (four) will seek to keep their slim hopes alive when they play later on Saturday (South African time).
The Springboks regained the Freedom Cup, a trophy played for by South Africa and New Zealand, for the first time since 2009.