In its first match since Football Federation Australia issued the club with a second show-cause notice over alleged salary cap breaches, Glory was largely outplayed by Newcastle but still managed to go second on the A-League ladder, only on goal difference to Melbourne Victory.
After scrambling in defence to keep the game scoreless in the first half, Perth led in the 50th minute via Andy Keogh's close-range header from a Jamie Maclaren cross.
Perth continued to hold out the Jets, who had 20 shots to Glory's 16, with desperate defence close to its goal-line before substitute Nebojsa Marinkovic put the result beyond doubt with a stunning strike in the 84th minute.
The win, however, could amount to nothing for Perth, who has until Wednesday to reply to the latest allegations of salary cap breaches.
FFA alleges Glory has failed to report payments and benefits to multiple players, leading to a significant breach of the $2.55 million cap in 2015.
If the allegations are true the mooted punishment is the loss of competition points.
While Perth has hit trouble off the pitch, the Jets' woeful season dived to a new low with a Hunter Stadium A-League record worst crowd of 4,162, admittedly in teeming rain.
Fans also vented their frustration with coach Phil Stubbins, holding up a banner which read 'Enough failure lies and arrogance 10,000 fans demand the muppet gone' at the start of the second half.
Stubbins said he understood the frustration of Jets supporters but he had hope and belief in his vision to rebuild the club for next season.
"The fans are obviously disgruntled and disappointed and I don't think I'm against anyone venting," Stubbins said.
"They're entitled to do what they feel is right.
"It's not really in support of the club, but as the head coach and someone who is at the front, then that vent and anger is going to go that specific person.
"We're trying to do everything we can behind the scenes to rebuild the club and hopefully come this time next year we're in a very strong position."
Meanwhile, despite the off-field uncertainty, Glory coach Kenny Lowe said his players remained focused on the job at hand.
"I think that's what we've shown all year," Lowe said.
"You mentioned character but I've stopped using the word because it got a bit boring, but I think they certainly deserve that epitaph."
On the salary cap allegations, Lowe said: "The club stated this week that all monies had gone through the books.
"If we were going to do something dodgy, why put it through your books?
"It doesn't sound a very sensible thing to do."
However, he said the coaching staff and players were not distracted by the drama.
"We're not bothered about that, we'll let the guys at our club deal with that," Lowe said.
"Let FFA come to their conclusion, then everyone will have a party one way or the other.
