Victory started well controlling the early possession but it was the visitors who hit the lead after just 11 minutes as a Shinji Ono free-kick found Iacopo La Rocca who easily finished the opener.
That goal stunned Victory who struggled to get back in to their rhythm especially without Archie Thompson there providing stability up front.
Despite that element of control, Marcos Flores had a good opportunity in the 20th but he looked for too much time allowing Western Sydney to recover.
The best chances were clearly with the visitors as Dino Kresinger, Ono and LaRocca all narrowly missed chances as Western Sydney took a 1-0 lead in to the break.
Victory's poor night nearly continued nine minutes after the break as Adrian Leijer inexplicably tried to do a back-pass without looking which allowed Youssouf Hersi in but Leijer was spared as he shot wide.
Western Sydney Wanderers did finally make it two in the 72nd minute as Hersi beat his defender and shot which was saved by Nathan Coe but only in to Ono's path allowing him a simple finish.
Three minutes later Victory brought the crowd alive and kept themselves in the match as Billy Celeski played Connor Pain through. The youngster used his speed to beat his marker and calmly fired home to claw one back.
Despite that goal it was too little too late as Western Sydney got a vital win for the Premiership credentials.
The win effectively establishes a two horse race for the Premiership as it puts the top two five clear of third while Western Sydney now trail by just one solitary point.