Otago defender Kane Russell put the New Zealanders in match contention, but his team could not overhaul their world top-ranked opponents.
The Australians grabbed an early 2-0 advantage with goals in the 24th and 37th minutes.
Russell got his team on the board in the 48th minute with a drag flick to cut the Australians' lead to 2-1.
The Kiwis fought hard to try to find an equaliser but were unable to produce a fairytale finish to their defender Nick Haig's 200th match.
The Kookaburras sealed their win one minute from full-time with a close-range strike.
Coach Colin Batch said the final result was disappointing but many positives came out of the series.
``It's obviously disappointing to lose a final like that.
``We fought very hard in the second half to get back into it and were in a position where we could've levelled the game, he said.
``Overall, I'm pleased with the new guys in the squad.
``They've experienced some high quality games both here in Melbourne and at the Transtasman Trophy.''
