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South Africa claimed the series 2-1 after posting 179 for six in their 20 overs and New Zealand fell well short, finishing on 146-9.
They needed another innings like the one from Martin Guptill, who smacked 101 not out in the second T20 match, but instead failed to establish any momentum to the innings as wickets fell at regular intervals.
Captain Brendon McCullum (25 off 22) shared an encouraging second-wicket partnership of 47 with Guptill (24 off 20) after the early loss of Rob Nicol but things fell apart once the pair departed.
James Franklin (16), James Neesham (12), Nathan McCullum (17) and Corey Anderson (12) all got starts but no one could kick on. The Black Caps were never really in the hunt as the home side squeezed the life out of the visitors.
Earlier, South Africa had got off to a slow start as the impressive Mitchell McClenaghan (2-24) and Ronnie Hira (1-24) bowled tightly but Henry Davids (68 off 51) and Justin Ontong (48 off 30) wrested the initiative and some big hitting from David Miller (28 off 12) and Farhaan Behardien (22 off 11) ensured they posted an imposing target.
"It's disappointing because we came into this match with high hopes," McCullum said.
"We obviously built up some good momentum after the East London game. For a fair amount of the game I thought we competed well but I guess some of those bigger moments South Africa grabbed and we were found wanting at times. In the end, the right team won the series."
There were at least some encouraging signs after the debacle in Durban, when New Zealand were rolled for just 86 in the first match. They came back and snatched a dramatic victory in the second match, thanks to Guptill, and were competitive in the third.
Attention now switches to the two-test series starting in Cape Town on January 2. New Zealand have a three-day warm-up match against a South African XI in Paarl starting on Friday night (NZT).