They will meet Melbourne City away next week before home outings against the Central Coast Mariners and Sydney FC round out their campaign.
Finishing outside the top two would force them on the road for a large part of the playoffs.
Wellington were without Vince Lia (hamstring) and fellow midfielder Albert Riera (suspension) today, while centre back Ben Sigmund was a late scratching due to a leg injury, which marked the first game he had missed this season.
Those withdrawals prompted a shuffle in personnel for the Phoenix with Michael Boxall sliding in to the heart of defence to join skipper Andrew Durante.
Alex Rodriguez deputised for Riera in front of the defence, while Roly Bonevacia and Michael McGlinchey made up the rest of the midfield behind a front three of Joel Griffiths, Roy Krishna and Nathan Burns.
But for all their attacking endeavour, the Phoenix were behind on the scoreboard after only 34 seconds as Gui Finkler gave the Victory an early lead.
Melbourne, who Merrick often refers to as the benchmark in the competition, brought a dangerous side with them, including Finkler, Besart Berisha and veteran striker Archie Thompson.
The Victory also named All Whites forward Kosta Barbarouses on their bench.
Wellington were dealt a blow after 30 minutes when Griffiths left the field with a suspected knee injury. The 35-year-old was later carted to hospital after being substituted; Kenny Cunningham took his place.
The early goal stunned the Phoenix who didn't play with their usual freedom, while the absence of Riera was particularly troubling as the Victory were able to make inroads on the counterattack.
Melbourne also defended strongly and Wellington lacked the final pass to create a goal as the sides went to halftime with the Victory in front 1-0.
Referee Kris Griffiths-Jones was inconsistent during the first stanza, which didn't help the flow of the game as a handful of players from both sides collected yellow cards.
The Phoenix finally warmed in to the match during the second half and enjoyed a consistent spell for the first 15 minutes but an own goal - against the run of play - from Durante gave the Victory a two-goal buffer.
Wellington have been fast finishers this season with goals frequently coming late in games but this seemed like too much of an obstacle to overcome as the clock began to work against them.
The ever-present Thompson then added Melbourne's third with a tap-in from close range, which settled the result as the Phoenix let go of top spot on the A-League ladder.
Wellington Phoenix 0
Melbourne Victory 3 (Gui Finkler 1, Andrew Durante 59 og, Archie Thompson 66)
HT: 1-0
