The match had been called off with light failing in Brisbane. Steve Smith finished unbeaten on 91 as Australia (5/248) won the match on DLS by five wickets. The AUS XI were 5-248 when the match was called off in the 44th over and the DLS target was 232 at the end of that over.
It was another fine knock from former skipper Smith, batting at three, who made his return to Australian colours this week from a year-long ban for ball-tampering.
David Warner, who was in imperious touch during the Indian Premier League, flopped again in opening the innings, out for two to follow his duck and 39 in the series.
For New Zealand, the unheralded Will Young smashed his second century in a row, mastering a top-notch Australian attack led by Pat Cummins and Mitchell Starc.
Opener George Worker chipped in with 59, while Cummins was the best of the bowlers, taking 4-32 off eight overs.
Cummins and Starc, who took one wicket, were playing together for the first time in three months as the latter returns from injury.
Australia won the series 2-1, claiming a close opening game at Allan Border Field by one wicket while their trans-Tasman rivals bounced back to easily take the second by seven wickets.
Australia play two more warm-up matches at Southampton, against England and Sri Lanka, later this month before opening their World Cup campaign against Afghanistan in Bristol on June 1.