Victory opened the scoring through Ryan Teague in the 14th minute but failed to make the most of their dominance and conceded via Damien Da Silva's own goal late in the first-half at AAMI Park.
In tense encounter, both teams had multiple penalty shouts either waved away or overturned by VAR.
Tony Popovic's Victory were on the front foot, with winger Daniel Arzani particularly lively, but for a second consecutive week were left to rue failing to bury their chances.
Victory had 18 shots, with seven on target, while Wellington failed to register a single effort.
Zinedine Machach forced a save from Phoenix keeper Alex Paulsen as early as the third minute and Arzani blasted over the bar not long after.
Victory broke through via a lovely team goal, Arzani picking out Nishan Velupillay, who danced along the dead-ball line then slipped through Jason Geria.
The full-back squared the ball for the arriving Teague to power home.
Ryan Teague (r) scored early but it was not enough to earn Melbourne Victory a win over Wellington.
Victory continued to press and Arzani forced another stop from Paulsen in the 25th minute.
Wellington screamed for a penalty in the 39th minute when Arzani clattered into Bozhidar Kraev, but referee Shaun Evans wouldn't be swayed, and there was no VAR review.
Two minutes later, Tim Payne burst down the right then slipped through Kosta Barbarouses.
The 300-gamer's tantalising cross forced a sliding Da Silva to play at the ball and the Victory defender toe-poked into his own net.
Shortly after, Wellington were awarded a penalty when Da Silva clattered Nicholas Pennington in an aerial challenge.
But following a lengthy review with VAR Kris Griffiths-Jones, the spot-kick was chalked off over a marginal offside decision.
Victory received a penalty of their own in the 55th minute when Lukas Kelly-Heald was ruled to have fouled Bruno Fornaroli, but that decision was also overturned following a review.
Arzani limped off on the hour, and eight minutes later substitute Ben Folami unsuccessfully appealed for a spot-kick after going down under pressure from Kelly-Heald.
Victory pushed for a winner, with Chris Ikonomidis and Teague having late shots but were unable to find the killer touch.
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