New Phoenix signing Joel Griffiths' goal-scoring instincts kicked in with perfect timing at the Hutt Recreation Ground, with the former Newcastle Jets striker scrambling the ball home in the 79th minute after Louis Fenton's tricky run and cross.
Three minutes later, Nathan Burns doubled the lead with a free header at the far post from Roly Bonevacia's free kick, sealing Wellington's spot at the top of the table - at least until Perth Glory plays Melbourne Victory in Saturday's evening game.
The points took Ernie Merrick's side to 36 points- equal with Perth Glory but ahead on goal difference.
The defeat dropped Adelaide United to fifth on 33 points.
Fenton, returning after a two-week concussion break, was tested down the right early, where former Real Madrid winger Miguel Palanca's pace and skill stretched the Phoenix defence.
Despite doubts around the fitness of skipper Andrew Durante after a calf knock earlier in the week, Wellington's back four held firm in an up-tempo first half, the hugely experienced Ben Sigmund producing a stand-out effort in the middle.
Both teams had their chances, Spanish midfielder Isiais relishing his return from a one-match suspension with some early stinging shots, and Sergio Cirio linking well with Bruce Djite up front for Adelaide.
Phoenix also created some promising opportunities, Alex Rodriguez slipping a series of beautifully weighted passes through for Roy Krishna while Burns was a constant threat down the right.
Adelaide's defence also looked solid, boosted by the return of central defender Nigel Boogaard from knee problems but missing the steadying influence of Osama Malik, sidelined with an ankle injury.
Timing proved problematic, both teams battling strong, gusty northerlies and a slippery surface from earlier heavy rain.
Adelaide edged the Phoenix in terms of possession, forcing three corners to none and sending in nine crosses to Wellington's three in the opening 45 minutes.
The weather closed in early after the restart, and although both teams continued to press despite the steady rain, the match looked destined for a scoreless draw until Grffiths and Burns's late interventions.
