Mackenzie Hawkesby converted a penalty in added time before half-time at Marconi Stadium on Friday to extend the Sky Blues' unbeaten derby streak to 11 games.
Wanderers captain Amy Harrison had given away the penalty after her arm made contact with the ball following a Sydney corner kick.
Indiana Dos Santos rubbed more salt into the hosts' wound in the 64th minute thanks to a clinical cutback by substitute Millie Farrow.
Sydney can finish the round as high as ninth (22 points) in the league in a boost to their slim finals chances, three points off sixth-placed Brisbane Roar with two games left of the home-and-away season.
The Sky Blues, defending champions and premiers, had started the match in 11th.
Meanwhile, Western Sydney - who have not beaten their local rivals since December 2019 - are all but set to finish last in the league for the third time (2014, 2018-19).
The Wanderers are 12th (15 points) after suffering their third-straight defeat, five points off table neighbour Newcastle.
It was all Sydney on Friday night, the visitors the more daring and creative side.
Led by Hawkesby, Ante Juric's outfit flexed their muscles to finish the first half with nine shots to one, seven of which were on target.
Wanderers young guns Sienna Saveska and Bronte Trew tried to pull one back for the home side with an attempt each in the 54th minute, but neither were convincing.
Trew was left kicking herself in the 77th minute after sending the ball wide in front of an open goal.
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