Despite having started all 26 previous regular season games, Phoenix striker Stein Huysegems was dumped to the bench for the contest, which was probably an indication of his future at the club.
The former Belgian international and the Phoenix have been locked in contract negotiations for the past few months and neither side seems likely to budge and an exit from the capital seems inevitable for the 31-year-old.
Huysegems warmed up a couple of times in the second half but was never summoned for playing duties.
After promising so much during a glittering run in the middle of the season, this was an ugly way for the Phoenix to end their first campaign under coach Ernie Merrick.
They looked disorganised in defence and missed the tenacity of centre back Ben Sigmund, who was hobbled by a thigh muscle injury and sat out the game.
Third-string goalkeeper Jacob Spoonley was given the gloves in the absence of regular custodian Glen Moss and looked composed as always, despite being hung out to dry numerous times by his back four.
After being down 3-0 at halftime, the Phoenix made things tougher on themselves when left back Shaun Timmins was given a straight red card for taking out Victory winger Kosta Barbarouses in the goal box.
Melbourne skipper Mark Milligan converted the spot kick and Wellington were left to battle through the final 30 minutes with 10 men.
Surprisingly, they didn't miss a beat with a man down and managed to hold their own during a dour final stretch as their season came to a sodden end.
A Jeremy Brockie stunner in the final minute at least gave the fans something to cheer about.
The last time Melbourne came to Westpac Stadium in January they were beaten 5-0, so they can head back to Victoria safe in the knowledge they got their own form of revenge as they build towards the playoffs.
For the Phoenix, they will just be hoping to end the season without the wooden spoon.
Melbourne Victory 4 (Archie Thompson 1, James Troisi 29, Gui Finkler 45, Mark Milligan 59 pen) Wellington Phoenix 1 (Jeremy Brockie 90+3) Halftime: 3-0