Five tries from the Kiwis appeared to be too much for the Kangaroos, despite the home side's bright start.
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Beau Scott scored Australia's first try in the first three minutes, giving the hosts the perfect start over their close rivals.
New Zealand matched whatever Australia did as Kevin Proctor levelled the scores up 14 minutes later.
The Kiwis' lead was short-lived as the Kangaroos went ahead thanks to Greg Inglis.
Lewis Brown brought New Zealand back into the tie at 12-12 after darting through and ghosting into a gap to equalise.
The score remained all square at half time but New Zealand were quicker out of the blocks at the restart, as Shaun Johnson was gifted a lucky deflection off an opposition player to sprint through and give the Kiwis their first lead of the match.
New Zealand capitalised on their lead minutes later, as Kieran Foran's cross-field kick was collected by Dean Whare, who doubled his side's score at 24-12.
Jason Nightingale rounded off the scoring 10 minutes from time to secure New Zealand's victory over Australia at the Suncorp Stadium in Brisbane.