Playing under interim boss Steve Kean for the first time, Victory was ahead in the 14th minute through Ben Folami's first goal in Australia's top flight, with Storm Roux heading home Jake Brimmer's left-wing corner to double its advantage.
James Troisi reduced the arrears for Wanderers by hammering in via the crossbar, but Folami had his second in first-half stoppage-time – a pinpoint Brimmer delivery and appalling Western Sydney marking again factors.
Brimmer saw a 63rd-minute penalty saved by Daniel Margush, who was let down again from the resulting corner as Dylan Ryan scored.
Jacob Butterfield then clattered in a brilliant long-range effort, meaning Graham Dorrans' 76th-minute spot-kick looked little more than a consolation.
Mitchell Duke converted Troisi's cross and substitute Nicolai Muller got in on the act, but Kean's men held on.