The Proteas, who will return to Hamilton next February to play neighbours Zimbabwe in their World Cup opener, had already wrapped up the series 2-0 with victories in the first two matches at Mount Maunganui.
The South Africans, having been put in to bat by New Zealand captain Brendon McCullum, were 157 for three when the rain started falling in the 31st over of their innings.
Conditions never looked like improving and the match was called off just before 4 p.m. local time .
South Africa wicketkeeper/opener Quinton de Kock was 80 not out when the weather intervened, having hit 11 fours in his 94-ball knock.
