Kyah Simon scored twice for the visitors and Tanya Oxotoby put the ball into her own net as Sydney took a three-goal lead before half-time, but an improved second-half showing from the Glory ensured there would be no repeat of the 11-0 thrashing earlier in the season.
Alen Stajcic's side dominated the first half, which ensured a victory that means the Sky Blues will have a home semi-final if they win at Brisbane next week.
Sydney remained in third spot with the win, but now holds an unassailable five-point gap over fifth-placed Newcastle and are just one point behind the Roar.
The Blues took the lead after just six minutes when the Glory defenders failed to clear a dangerous Kylie Ledbrook cross and Oxotoby put the ball off the post and in for an own goal.
The visitors put Perth under significant pressure in the opening 15 minutes and were rewarded with their second goal when sloppy Glory defending gifted their opponents a corner and Simon headed it in after a goal-line scramble.
Sydney's pressure didn't ease up after the second goal as they continued to dominate territory and forced several good saves out of Perth goalkeeper Mackenzie Arnold.
Any hope of an unlikely Glory comeback was then put to bed on the stroke of half-time, when Jamie Harnwell's side again failed to clear and Simon tapped in her second from close range.
Perth lifted significantly after the break and nearly got one back when Katie Holtham worked her way into a good position, but the attacker shot just over.
The strong breeze which helped Sydney's cause in the first half was making it difficult for them to get it out of their own half in the second, but they still created several chances.
The best opportunity for the Sky Blues to add a fourth came in the 74th minute when Caitlin Foord was played through but Arnold did brilliantly to force a goal kick, before Perth were denied a penalty for an apparent handball with 10 minutes left.
Glory, which has just three points from nine games, finishes their season next Saturday with a home fixture against the Jets.
Perth Glory 0 (Oxtoby 6 og)
Sydney FC 3 (Khamis 22, Simon 45)