Glory led 3-0 thanks to a corset for the first goal of the season by Joel Chianese and Brendon Santalab at halftime on Wednesday.
Sydney forward Adam le Fondre retired one in the 68th minute with a stunner from outside the box, but the increase in visitors was too late.
The result broke Glory's nine-game losing streak against Sydney in the league.
But more importantly, he lifted Glory by six points from both Sydney and Melbourne Victory in the race for the premiers' plate.
The victory suffered a 2-0 loss to Adelaide earlier in the day.
Sydney entered the game after posting six wins and a draw in his last seven trips to Perth.
But their hosts showed little fear against their bogey team, unleashing a powerful display in the first half that surprised their park rivals against 9521 fans.
The destruction began in the 13th minute when a smart one-two between Jason Davidson and Diego Castro broke the Sydney defense.
Chianese then stretched her leg to put Davidson's cross home.
The visitors protested against Chianese's second goal in the 24th minute, claiming that the speedy attacker handled the ball before scoring.
Chianese did well to control Neil Kilkenny's long ball with his chest, but the Sydney players felt that the ball touched Chianese's arm when it bounced again.
Sydney stumbled in the third minute of halftime in the first half, when a defensive rotation allowed Santalab to jump for his first Glory goal.
The introduction of Danny De Silva in the 66th minute gave Sydney a much needed spark, and Fondre scored his 11th goal of the season two minutes later.
But it turned out to be nothing more than a consolation goal.
Glory coach Tony Popovic made a whopping six changes in his starting lineup in an attempt to rest the players during the busy period.
Juande, Castro and Matthew Spiranovic were among the ins, while Santalab got his first start of the year instead of Andy Keogh.
Keogh, who could be part of a direct exchange for Melbourne City striker Bruno Fornaroli, was named on the bench and entered for Santalab in the 64th minute.
Sydney coach Steve Corica named an unchanged XI for the team that destroyed the Central Coast 5-2, but in the first half they seemed out of step despite having two more days of recovery time than Glory.