Both teams had their chances in the second spell after sharing honours with a goal apiece in the first half.
But it was Daniel McBreen's missed penalty in the 70th minute that proved the most costly, as the Phoenix extended their unbeaten run to four games.
Winds gusting up to 100km/h swirled around the stadium, making life difficult throughout, and both teams struggled for accuracy early on.
Wellington's back four came under increasing pressure as the game progressed, with Joshua Rose proving particularly troublesome down the left and McBreen dangerous on the edge of the area.
The visitors continued to work the ball around, with their movement off the ball in the front third providing plenty of options.
Accuracy and pace gave the Mariners a well-earned lead after 15 minutes when Nick Fitzgerald slipped a beautiful through ball for Matt Simon to blast home into the top right from 15 metres out.
The Phoenix regathered, Kenny Cunningham and Stein Huysegems forcing Mariners keeper Liam Reddy into two quickfire blocks at the half-hour mark, but the Mariners looked set to take a 1-0 lead into the break until Cunningham struck a minute out from the halftime break.
Sharp work from the midfield found Cunningham just outside the box, and the Costa Rican squirmed around Storm Roux before finishing with a well-placed strike past the diving Reddy.
With the wind at their backs in the second spell, the Phoenix pressed hard, but weren't able to convert their half-chances.
Those lost opportunities looked costly in the 70th minute, when referee Matthew Gillett ruled keeper Glen Moss had brought down the hard-working Trent Sainsbury in a rare Mariners foray forward.
But McBreen's goal scoring woes continued - last year's Golden Boot winner has just one this season - and he blasted the resulting penalty sky-high.
The Phoenix kept working hard, finishing on an up-tempo note in front of a boisterous 7005-strong home crowd.