The All Blacks raced into a 20-0 lead before half-time, only for the Wallabies to clamber back to within a point with an impressive second-half recovery.
But Auckland wing Howlett's third finish proved enough, and aided by an impressive kicking display by substitute Luke McAlister, the All Blacks were home and dry.
Fly-half Leon MacDonald, a try-scorer in Dunedin against South Africa, passed a late fitness test, but was replaced by McAlister after a kicking error early in the second half.
He took his place in a starting XV with two changes - Howlett and Sione Lauaki coming in for Rico Gear and the suspended Jerry Collins.
For their 400th Test match the All Blacks reverted to their traditional 'Ka Mate' haka after last week's new-look war dance.
But it was Wallaby captain George Gregan who took centre stage, earning a world record-equalling 114th cap.
New Zealand dominated the opening exchanges, penning the Wallabies behind their own 22.
MacDonald put points on the board in the 13th minute, kicking a penalty after English referee Chris White spotted an infringement from George Smith.
And the All Blacks soon added their first try of the night. On the quarter-hour mark, Rodney So'oialo stole a line-out and Ali Williams went on a storming run.
Tana Umaga collected the ball, and set up flanker Richie McCaw to pound home from short range. However, MacDonald missed the conversion.
Five minutes later, a touch of inspiration from an unlikely source extended the All Blacks' lead.
Lock Williams chipped a free-kick from under the posts out wide to the right.
Howlett caught the ball and made an easy touchdown, but MacDonald failed once again with the extra points.
The visitors' first chance to reply came from a Mat Rogers penalty on the right wing, but the makeshift number 10 squandered the opportunity.
And not long after that miss, Howlett grabbed his second try of the night. Quick passing across the backline gave the wing an easy chance, and Lote Tuqiri's diving tackle was not enough to stop the marauding Aucklander on his home ground.
Australia hit back when Gregan supplied Matt Gerrard. He took out Piri Weepu before supplying lock forward Mark Chisholm for his fourth Test try.
Rogers missed again with his conversion attempt but Australia were beginning to gain some momentum and at the start of the second half they halved the deficit.
Chisholm won a long line-out, setting up Rogers to supply Gerrard, whose straight running through the backline saw him crash over for Australia's second try.
And within three minutes, a MacDonald kick was charged down and Tuqiri scored to help peg the lead back to a solitary point at 20-19.
Henry decided something needed to be done and he replaced MacDonald with McAlister, and the coach was rewarded when the substitute slotted home a penalty soon after his arrival to increase the lead to 23-19.
Mat Dunning, a replacement for Australia, then conceded another penalty to allow McAlister to open up further space between the two rivals.
A third success for McAlister came on the hour-mark, this one an imperious effort from 51 metres out wide on the right.
A clash of heads with Aaron Mauger forced Australia's South African-born back Clyde Rathbone out of the action, and moments later his replacement, Lloyd Johansson, made a dream debut with a try.
The youngster finished off a sharp passing move involving half-backs Gregan and Rogers, plus loose forward Smith. Rogers again missed the conversion but Australia were still alive in the match as they sought to avoid their fifth successive Test loss.
However, the outcome was sealed eight minutes from time, when from Mils Muliaina's kick and James Ryan's good foraging work, Howlett picked up a loose ball to complete his treble.