Kevin Muscat's hosts led twice in the clash at AAMI Park on Sunday, but on each occasion they were pegged back, before conceding again to suffer their first home loss to the New Zealand outfit.
The result comes as a long overdue measure of revenge for Phoenix coach Ernie Merrick, who was sacked by Victory in 2011 despite having led the club to two titles.
And by surprising the Big V in their own backyard this weekend, the Nix have dealt a blow to Victory's hopes of adding to that haul of silverware in 2014-15.
GOALS
1-0 (Scott Galloway 34')
Galloping down the left flank, Galloway's ball inside found Besart Berisha. The Albanian couldn't control it but the rebound fell straight to the left-back, who fired a firm, low shot between the legs of Glen Moss and into the back of the net.
1-1 (Roly Bonevacia 42')
A stunning free-kick drew the visitors level shortly before half-time, the Dutch midfielder curling an inch-perfect finish into the top right-hand corner of Nathan Coe's goal. Did the Victory keeper move a fraction late?
2-1 (Kosta Barbarouses 54')
A move which started with Jason Geria carrying the ball down the right flank and finding Barbarouses ended in Carl Valeri slipping the winger in behind the Phoenix backline, where the in-form New Zealand international prodded a confident finish past Moss.
2-2 (Michael Boxall 68')
Bonevacia hung up an inviting free-kick at the back post and Boxall rose unchallenged to head the ball down and into the back of the net.
2-3 (Nathan Burns 77')
Boxall received a throw-in just inside the Victory half and raced away from Nick Ansell with ease. Burns appeared to be miles offside but was deemed to be in a passive position until the ball was played back to him by the galloping fullback, at which point he became active, with neither referee nor lineman taking issue with the Socceroo forward's close-range finish.
HIGHLIGHTS REEL
The introduction of fan favourite Archie Thompson in the 73rd minute drew a huge round of applause from the Victory faithful, as the club stalwart notched his 200th appearance in navy blue and white.
BACK TO THE DRAWING BOARD
A team with genuine title aspirations can't afford to give away as many goals to set-pieces as Victory have this season. Coe might perhaps have done a little better with Bonevacia's goal, while the marking was dubious to say for the least for the Phoenix's second. Ansell allowed Boxall to turn and get away from far too easily for the winner.
THE FINAL WORLD
Next up for Victory is a huge showdown with Glory, a game which could be prove to be decisive in determining the destination of the Premier's Plate. The Phoenix meanwhile are at home to fellow finals hopefuls Adelaide United.
TEAMS:
Melbourne Victory: Coe, Geria, Broxham, Ansell, Galloway (Georgievski 89'), Valeri, Milligan (Delpierre 80'), Barbarouses, Finkler (Thompson 73'), Ben Khalfallah, Berisha.
Wellington Phoenix: Moss, Boxall, Sigmund, Durante, Muscat, Riera, Bonevacia, Rodriguez, Krishna (Griffiths 61'), Burns (Lia 95'), McGlinchey (Hicks 92').
Scorers: Galloway (34'), Bonevacia (42'), Barbarouses (54'), Boxall (68'), Burns (77')
Red cards: None
Yellow cards: Sigmund (16'), Berisha (32'), Milligan (67')
Conditions: 21 degrees, sunny
Attendance: 22,096 @ AAMI Park