Jason Petkovic's brilliant save from John Markovski's header changed the course of this mixed bag of a match.
Petkovic made an instinctive save from Jonesy's close range effort and kept the scoreline at 1-1.
That allowed Brad Hassell to snatch all three points for City when he knocked in the loose ball after Milanovic's free kick had a hit a post.
City had gone ahead when Tobin touched in a corner which Glory keeper Milosevic should really have dealt with.
Adelaide had been nullifying Perth and seemed content with a point and certainly attempted to shut up shop once they were ahead.
Markovski and Boutsianis were thrown into the fray from the bench after being dropped from the starting line-up, and Boutsianis provided one of his free kick specials to level the scores.
The game swung Glory's way and Markovski's header was one of two great chances the big striker failed to take.
Then home debutant Craig Deans' only error of the game saw Hay forced into a rash lunge on the edge of the area. As Mori decoyed with a long run up, Ivanovic stepped in to take a curling free kick which hit the right hand post and Hassell reacted ahead of a static Glory defence to grab the glory for City.