De Villiers won the toss and was keen to bat first on a hard track under clear skies at Westpac Stadium. He played his part with a rapid 85 off 80 balls in which he became the fastest batsman to amass 9,000 ODI runs.
He reached the milestone in his 205th innings, outperforming the previous record of 228 held by India's Sourav Ganguly.
But apart from Quinton de Kock, who posted his fifth consecutive half century, 36 from Faf de Plessis and 35 from Wayne Parnell, no other South African batsman was able to seriously better a controlled New Zealand bowling effort.
Amla never looked comfortable and struggled to seven off 19 before his departure saw du Plessis and de Kock accelerate the scoring in a 73-run stand before both fell four balls apart in the same Colin de Grandhomme over.
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Jimmy Neesham took a well-judged running catch on the boundary to put a full stop to de Kock's innings at 68.
With Parnell propping up one end, de Villiers was able to boost the score in an 84-run partnership before both fell in the final over.
Parnell was adjudged run out on the last ball of the innings after grounding his bat legitimately but then lifting it as the bails were removed. De Grandhomme, who completed his 10 overs in one spell, returned the best New Zealand figures of two for 40.