The Parramatta hosts were on the back foot for much of the first half, but improved after the break and claimed the game's only goal through Mark Bridge in the 82nd minute.
Labinot Haliti cleverly slipped around his opposite man and fired a lethal pass across the face of goal to an unmarked Bridge, who slotted the ball home from the far post to spark wild celebrations.
There were some nervous moments for the 15,854 fans who braved the rain as the Victory desperately searched for an equaliser, but Kevin Muscat's men were unable to avoid a second straight defeat.
The win lifts the Wanderers to the top of the A-League ladder, two points clear of Brisbane Roar who play Newcastle Jets on Sunday.
Adelaide United eased the pressure on coach Josep Gombau with a gutsy 1-1 draw at Perth Glory.
Gombau's side claimed a first point in three matches, but had opportunities to claim their second win of the season.
United's Osama Malik and Glory substitute Chris Harold each scored second-half goals from corners in front of 8,754 fans, many of whom had come to see French star William Gallas make his A-League debut.
Gallas was introduced in the 62nd minute to loud cheers from the Perth crowd, eight minutes after Malik had put the visitors ahead by converting a fabulous cross from Fabio Ferreira.
An unmarked Harold equalised in the 70th minute, heading past Eugene Galekovic to extend Adelaide's winless streak to five games.
