Victory got to grips with the wet conditions quickest, opening the scoring after Nick D'Agostino was set up by former Phoenix favourite Marco Rojas.
The spectre of another heavy defeat loomed as the Victory dominated the opening exchanges but the visitors gradually gained a foothold before receiving a double lifeline back into the match.
Reno Piscopo won a 20th-minute penalty when his ball into the area was handled by Josh Brillante. Piscopo's poor penalty was saved by Ivan Kelava but he won a second spot kick in the aftermath after copping an elbow to the head from Leigh Broxham.
There was no doubt about the first penalty; the second, less so.
Gael Sandoval stepped up for the second attempt — Kelava again dived to his right and almost pulled off a second save but the Mexican's penalty but better placed than Piscopo's and nestled in the side netting.
The first-half double penalties proved a prelude to further spot kick drama around the hour mark that was almost comical.
D'Agostino thought he'd netted his second off a rebound when keeper Oli Sail pushed an awkward bouncing Jake Brimmer shot back out towards him. Seven minutes later, the Victory's lead was finally confirmed.
The interim saw the VAR direct referee Shaun Evans to a sideline screen where he first disallowed the goal for an earlier foul on Ben Old but then awarded the hosts a penalty for an even earlier hand ball by Louis Fenton. Brimmer finally put the hosts back in front from the spot.
Wellington coach Ufuk Talay, who was booked soon after, probably would have traded the initial goal for the seven lost minutes.
But thoughts of a second Phoenix equaliser were undone when an unmarked Rojas headed in a superb Jason Davidson cross at the far post 10 minutes later.
Melbourne Victory 3 (Nicholas D'Agostino 2, Jake Brimmer 68 pen, Marco Rojas 78)
Wellington Phoenix 1 (Gael Sandoval 26 pen)
Halftime: 1-1
