Adam Le Fondre beat Vedran Janjetovic at the second attempt in the fourth minute as Steve Corica's side made an enterprising start at the Sydney Cricket Ground.
Oriol Riera passed up a good chance to equalise before half-time and Sydney captain Alex Brosque left the Wanderers with a mountain to climb when he fired home in the 53rd minute.
Western Sydney thought it was back in the contest with an hour played when Roly Bonevacia picked out the bottom corner but referee Chris Beath decided to consult the video official.
A seemingly minor infringement, where Jaushua Sotirio inadvertently blocked Sydney left-back Michael Zullo, was deemed enough for Beath to rule out the goal and Wanderers head coach Markus Babbel was apoplectic.
The former Germany defender hurled his coat to the turf and unleashed a verbal volley towards the officials. Beath showed Babbel a red card, leaving him with a long trudge back to the SCG's famous old pavilion after booting an advertising triangle.
That flashpoint appeared to fire up his side and the Wanderers finished strongly, with Jordan O'Doherty curling a superb strike against the post before a hamstring injury to substitute Siem de Jong forced Sydney to conclude the match with 10 men.
Earlier, Dario Vidosic levelled six minutes from time to give Melbourne City a 1-1 draw at Central Coast Mariners.
Ross McCormack opened the scoring midway through the first half against his former club, slotting in at the near post, but substitute Vidosic pounced when the Mariners, who will now turn their attentions back towards the Usain Bolt saga, failed to deal with a corner.