However, some tremendous goal-line defence repelled the Kiwis with Kevin Locke and Lewis Brown going close to scoring.
Australia crossed the line again 11 minutes before the interval when Williams bulldozed his way over with Thurston adding his second conversion.
Thurston came in for someone special attention from the Kiwis, with Jared Waerea-Hargreaves seemingly on a one-man mission to ruffle the Queensland halfback's feathers with three huge hits.
Matt Scott took exception to another late shot from Jeremy Smith with both sets of players joining in a mid-field melee that resulted in an Australia penalty.
Thurston reacted in the best possible manner with a well-worked try on the stroke of halftime thanks to a superb burst from Williams to give his side a comfortable advantage at the break.
The Kiwis started the second period much better than the first, with a Jason Nightingale try seven minutes after the restart.
A booming kick from Kieran Foran was flicked back into his own goal area by Chris Lawrence, under pressure from Locke and Gerard Beale, and the St George Illawarra winger reacted quickest to touch down.
The home crowd, very much behind the world champions, were on their feet again in the 55th minute following a high-class try finished off by Kalifa Faifai Loa.
Benji Marshall kept the ball alive superbly and Mannering, Nightingale and Beale combined to send the North Queensland winger through to score.
Marshall added the extras to close the gap to six points but Tim Sheens' men eased the pressure with a fourth try scored in the left corner scored by Darius Boyd.
Akuila Uate then rubber-stamped the victory by getting a hand to a Billy Slater grubber-kick five minutes from the final siren.
Luke could find himself in hot water by the match review committee after poleaxing David Shillington with a cannonball challenge low down on his legs in the second half.
Shillington managed to walk off the field, but looked in great pain and could be in doubt for next week's clash with England at Wembley.
Australia 26 (D Boyd M Scott J Thurston A Uate T Williams tries J Thurston 3 goals) def. New Zealand 12 (K Fai Fai Loa J Nightingale tries B Marshall 2 goals) at Halliwell Jones Stadium.
- AAP