Kane Williamson guided the home side to the 2-nil series win in making his 32nd test century and finishing 133 not out.
He put on 152 for the fourth wicket with Will Young who made 60 not out, as New Zealand won the inaugural Tangiwai Shield.
Having enjoyed a comfortable 281 run in the first test in Tauranga, the Black Caps had to work hard for victory in the second test.
They trailed by 31 runs on the first innings after South Africa posted 242 batting first and then dismissed New Zealand for 211.
But after being 202-4 in their second innings they were unable to kick on and were dismissed for 235, losing their last five wickets for addition of just 33 runs.
That left New Zealand requiring 267 for victory and at 117-3 the tourists were still well in the match.
However the Williamson and Young ground down the Proteas to deliver the victory with a day to spare.
Seddon Park has been a happy hunting ground for Williamson having now scored six test centuries at the venue, including his highest total of 251 which came against the West Indies in 2020.
He's scored scored three centuries in his four innings with 118 and 109 in the first test in Tauranga and today's knock of 132 not out.
The win extends New Zealand's lead at the top off the ICC test championship standings.
