Though Kenny Lowe's men gave their all in front of a crestfallen home crowd, it came as no surprise to see them come unstuck with all incentive to excel now gone after Football Federation Australia's swingeing punishment ruled it could finish no higher than seventh on the ladder.
The win moved Graham Arnold's men up to joint top alongside Melbourne Victory but behind it on goal difference, with Glory also on 44 points pending its enforced drop down the table.
A brace from Sky Blues captain Alex Brosque, sandwiched between a spectacular effort from Bernie Ibini, did the damage.
Lowe admitted FFA's decision was hard to take so close to kick-off.
"They're going to be disappointed. They've worked ever so hard to get into a fantastic position," Lowe said of his players
"But we're professionals. We get paid to do a job. As hard as it is, that's what we're going to do for the next two games.
"You're disappointed, but you can't let yourself down. Everyone is in this together. We'll probably feel a bit sorry for ourselves in the next day or two.
"But we've got two days off, we'll come back into training, and bang back at it again."
All too aware of Perth's predicament, Sydney was full of intent straight from the kick-off and Chris Naumoff came close with a crisp header after Nikola Petkovic's cross had dropped invitingly into his path.
But, with pride on the line if nothing else, Glory refused to roll over and showed a grim determination in seeking to keep the Sky Blues at bay.
But it took more than an element of luck for the home team to retain parity when, in the 19th minute, midfieder Milos Dimitrijevic saw his superbly struck shot from just inside the penalty area come crashing back off keeper Danny Vukovic's crossbar.
Then Ibini crossed for Golden Boot front-runner Marc Janko to send a scissors kick just wide.
Moments later Ibini set Brosque free and he brought a fine save from Vukovic.
The goal Sydney had been threatening came in the 35th minute when Petkovic burst down the left and crossed for Janko, whose header was only parried by Vukovic, and Brosque swept home the rebound for his fourth goal of the season.
The sense of injustice swirling around the stadium over Perth's plight was heightened a minute later when Olyroos striker Jamie Maclaren thought he had levelled the scores with a clever finish from the edge of the area, only for a linesman's flag to be raised to rule it out.
Television replays showed that Glory was hard done by with Maclaren appearing to be in an onside position when the ball was played into him.
Sydney turned the screw after the break with Ibini lashing home a stunner from the edge of the area on the hour and then Brosque netting his second five minutes later after exchanging passes with Ibini.
Perth's night was symbolised by a header from Richard Garcia which instead of going in came back off the woodwork.
Arnold said FFA's announcement even distracted his players.
"They were talking about it at the pre-match meal and I had to refocus them, and pretty much tell them it's got nothing to do with us," Arnold said.
"We have to be professional in what we do. I thought tonight was a very good performance from us."
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