The White Ferns have lost the third and final T20 in Brisbane to be whitewashed and head into the Women's T20 World Cup struggling.
The match was closer than previous games, but still a win for the home side by five wickets with five balls to spare.
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Winning the toss and choosing to bat first, New Zealand put up a total of 146. Amelia Kerr and Georgia Plimmer scored the bulk of runs with Plimmer getting her maiden T20I fifty, a 48-ball 53 and hitting five fours and a six in the process.
She was supported by Kerr who scored 40 off 36 balls, but once the partnership was broken, Australia managed to restrict New Zealand to 146/6 in their allotted overs.
Suzi Bates made 19 opening the innings and Maddy Green 12 down the order, but otherwise no other player reached double figures, while extras were 11.
In response, the hosts lost both Mooney and Healy early in the chase but never really let the situation go out of their hands.
Georgia Wareham was promoted to bat at No.3 and she responded with a quickfire 26 off 16 balls. Ashleigh Gardner and Ellyse Perry then followed it up with handy knocks of 33 off 26 and 36 off 29 respectively to put an end to any hopes of New Zealand victory.
Eden Carson took two wickets for 29 from her four overs while Hannah Rowe, Fran Jonas and Kerr took one each.
New Zealand will play World Cup warmup matches in Dubai next week against South Africa and England before their opening pool game against India, on 5 October.