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The victory, secured via a John Aspropotamitis own goal just after half-time and Riku Danzaki's ninth goal of the season, lifts the Roar to third on the ladder with one regular season fixture to play.
The result means Perth cannot make the top six, sitting five points adrift of sixth-placed Adelaide United ahead of Saturday's trip to Newcastle which is now a dead rubber.
It also ensures Western Sydney will have a fourth-straight season without a finals appearance, Carl Robinson's eighth-placed Wanderers now unable to close the gap to the top six ahead of Thursday's clash with Adelaide.