Needing only a losing bonus point to secure the southern hemisphere's premier title, South Africa finished their campaign in style with their fifth win in six Tri Nations games.
Morne Steyn and namesake Francois kicked 22 points for the visitors, with Fourie du Preez and Jean de Villiers grabbing tries - the later on his final international appearance before departing for Magners League champions Munster.
The Boks raced into a 22-12 half-time lead before the All Blacks threatened a late come back in an attempt to take the tournament down to the final fixture when they travel to Australia next weekend.
But Peter de Villiers' men held their nerve to record their third successive win over New Zealand and their 11th victory in 13 tests in the past 12 months.
The Boks' only two defeats since the final game of last year's Tri Nations have come in the third and final Test against the Lions in July and last Saturday's 21-6 reverse at the hands of the Wallabies in Brisbane.
"It was as tough as it gets," said Bok head coach de Villiers after his side broke New Zealand's dominance of the competition since 2004.
"The All Blacks aren't a walkover. To play them in their backyard, it's a great honour to come out victorious.
"We did find something in Hamilton - we have the Tri-Nations Cup."