Newcastle hit the front mid-way through the first half after Carney intercepted an Anthony Golec pass and fired past Glory goalkeeper Jerrad Tyson.
The home side was holding on and giving its loyal supporters something to cheer about.
But in the dying minutes Sidnei stepped up to equalise for Glory.
The contest was forced into extra time, but it didn't take long for Perth to go in front after it was awarded a penalty and Nebojsa Marinkovic slotted in the spotkick.
Just as looked it as though the visitor would triumph, the Jets, who were pushing hard, equalised through Labinot Haliti to force the contest into a penalty shootout.
In the shootout, Jerrad Tyson made an incredible three saves for Perth, which gave Gyorgy Sandor the chance to win it.
He made no mistake to secure a last 16 spot for the West Australian side.
