Tony Popovic's side are rooted to the foot of the table after a dreadful campaign, and suffered their eighth defeat in 12 outings in a hugely entertaining clash at the Pirtek Stadium.
Carl Valeri put the Victory ahead with a stunning strike midway through the first half - his first goal for the club.
But Western Sydney fought back admirably, and levelled 10 minutes into the second half through Nick Kalmar.
The game looked set to end in a draw, but Melbourne snatched a valuable three points courtesy of Gui Finkler in the 80th minute.
A superb counter-attack from Kevin Muscat's men ended with Finkler finishing clinically from close range to earn a win that moves the Victory above Adelaide United and into joint second in the A-League standings.
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