The 30-year-old De Villiers, however, completed his 39th ODI half-century, while Duminy compiled his 20th and hit a six to win the game as they tourists finished on 236 for four, having chased New Zealand's 230.
The series is being used by both sides to finalise their selections for next year's World Cup in New Zealand and Australia.
New Zealand's batsmen, however, did little to showcase their credentials and their total was only boosted by a record 10th-wicket partnership of 74 between Luke Ronchi and Trent Boult which rescued them from 156 for nine.
Wicket keeper Ronchi was agonisingly close to his first ODI century after reaching 99 on the final ball of the 45th over.
The 33-year-old, however, seemed in two minds on the next ball and only succeeded in giving wicket keeper Quinton de Kock his fifth catch of the innings and sixth dismissal overall with the stumping of Tom Latham.
The innings by Ronchi, under pressure from test wicket keeper BJ Watling for a place in the World Cup squad, showed coach Mike Hesson he could be the ideal player to close out New Zealand's innings after hitting three sixes and 11 other boundaries in his 83-ball stay.
(Reporting by Greg Stutchbury in Wellington; Editing by Ian Ransom)
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