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Set up by a brilliant 145 not out by Kane Williamson, the Black Caps, with the help of a record-equalling five run outs, completed a 27-run win to take out the three-match series with one game remaining.
Following a 2-1 defeat in the Twenty20s and a 2-0 thrashing in the test series, New Zealand bounced back to make history with their first ever series win in South Africa in any format of the game.
They will chase a rare series sweep in the third and final one-day international in Potchefstroom on Saturday morning (NZT).
Skipper Brendon McCullum, who took over what seemed to be a poisoned chalice from Ross Taylor before the tour, rated the historic series-clinching victory as one of New Zealand's "biggest ever wins in the limited overs game".
"I'm not going to underplay it. It's a phenomenal effort, really, to come over here as the ninth-ranked team in the world against the No 1 team in their own conditions and to be 2-0 up in the series is incredibly satisfying and will probably go down as one of our biggest ever wins in the limited overs game. It's obviously a nice way to be finishing off the tour after a pretty tough time."
McCullum had plenty of praise for Williamson, who not only made the highest individual score by a New Zealander against South Africa but also the sixth-best in this country's one-day history. It was the highest score by a Kiwi against one of the major test playing nations - Lou Vincent tops the list with his 172 against Zimbabwe in 2005.
"Kane Williamson's innings was as good an innings as I've ever seen by a New Zealander in one-day cricket," McCullum said. "I think a few guys backed it up around him as well and I thought the way we were in the field was outstanding."
Williamson was composed throughout his innings of 145 from 136 balls, despite suffering cramp towards the end of his 207-minute stay at the crease.
"It was obviously nice to contribute like that in such an important game but I think the second half of the match was pretty key with all the run outs in the field on a very good wicket," the 22-year-old said of his third ODI ton.
"It's been tough alright playing the No 1 team in the world and the boys really stepped up in the last two games and it's really rewarding to come home with a series win."
Williamson hit 17 fours and a six off the last ball of the innings for his career-high score and he shared a 127-run partnership with Grant Elliott (48).
Few others contributed, however, with Nathan McCullum the next highest scorer with 19.
They lost Martin Guptill for a duck without a run on the board and took three and a-half overs to score their first runs.
The Proteas seemed in the box seat in their chase when 167-1 in the 30th over but lost Graeme Smith (66) and Colin Ingram (79) within four overs of each other, which proved to be the turning point as the Black Caps took control.
Kyle Mills finished with the impressive figures of 2-28 from nine overs but it was the New Zealand fielding effort that constantly did the damage with Nathan McCullum and Guptill both involved in two run outs each.
The total of five run outs in the South African innings equalled the one-day record, shared by nine other teams and the first time New Zealand had achieved the feat.
- Cameron McMillan of nzherald.co.nz