Having won its first game when the league resumed last month, Glory then suffered back-to-back losses to dent its hopes of a top-six finish.
However, it went ahead at Bankwest Stadium on Tuesday as Jake Brimmer's deflected effort fell into the path of Ivan Franjic, who marked his 50th Perth appearance with a 60th-minute opener.
Wanderers hit back through Mitchell Duke three minutes later, but Dylan McGowan then handled in the area, allowing Neil Kilkenny to restore Perth’s lead from the spot.
Substitute James Meredith lashed in a brilliant third from the edge of the box to tighten the Glory’s grip on fifth place.
The Wanderers remain down in ninth, four points outside the top six with two to play.