Hurricanes centre Conrad Smith celebrated his return to action from injury when he came on for the second half and scored a try to break a 17-17 scoreline with three minutes left in the game.
The Highlanders led by seven points with about 15 minutes to go but couldn't sustain their defensive efforts to fall to their second close defeat in as many games.
The Hurricanes notched their first win of the season, after mistakes and infringements threatened to see them let the game slip.
The first half was a drab affair as both sides struggled in greasy conditions to get their games flowing.
It was not until the final minutes of the half that Wellington took the lead with a penalty by first five-eighth Daniel Kirkpatrick after Highlanders flanker Adam Thompson had been sinbinned for flopping over the ball.
The Hurricanes took advantage of a 14-man Highlanders who were without All Black Thompson early in the second half.
All Blacks Smith and Ma'a Nonu came off the bench for the second half and Nonu immediately made his mark with a powerful line burst to put them on the front foot.
The Highlanders missed their first tackles of the match as Nonu's next line break set up a try in the left corner for winger David Smith. The try was converted from the side line by Kirkpatrick.
But 10 minutes later, Highlanders first five Dan Bowden got his boot onto a loose pass from Nonu around the half way mark.
He beat Hurricanes lock Jason Eaton to the ball to ground it over the line.
Minutes later the Hurricanes let the ball bounce Highlanders No 8 Steve Setefano pounced on the loose ball for an easy run to dot it down by the posts for Bowden to convert.
Bowden added a penalty to give his side a seven-point lead.
The Hurricanes finally held on to the ball long enough to pound away at the Highlanders line which finally buckled for Eaton to dive across between two defenders.
Piri Weepu converted to tie the scores.
Weepu, who had shifted to first five with Alby Mathewson coming in at halfback, set up the winning try.
He booted the ball ahead and then recovered it as Highlanders defender Ben Smith fumbled the collect.
Weepu relayed the ball to Smith who crossed near the corner flag.
Highlanders match skipper Jason Shoemark said his side had made started making silly mistakes at crucial times.
"We had the game there and we just had to play field position.
"We couldn't get out of our own half in the last ten minutes and the Hurricanes are going to punish you sooner or later.''
Hurricanes match skipper Tamati Ellison said the conditions had not helped and both side dropped the ball at crucial times.
"We battled a wee bit tonight. We would have kicked the ball a lot more but in the conditions we couldn't and the ball slipped out in a few carries.
"We also didn't put enough pressure on the Highlanders in the kick and kick chase.''
