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.
Scott Galloway handed the home side the advantage just past the half-hour mark, only for Roly Bonevacia's stunning free-kick to draw Wellington just before the break.
Kosta Barbarouses restored Melbourne's lead, but goals from Michael Boxall and Nathan Burns settled matters.
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.
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