City almost extended their winless run to three matches despite dominating possession and enjoying the bulk of chances, with star attacking trio Jamie Maclaren, Mathew Leckie and Andrew Nabbout again kept goalless.

But just eight minutes after entering the fray, Joe Marston Medallist Atkinson headed home in the 88th minute to snatch all three points.

"We were very good. We dominated the whole 90 minutes and eventually we got rewarded for that," City coach Patrick Kisnorbo said.

"Football is about opinions. At the end of the day, we hit the post and we had the goal disallowed by 30 centimetres.

"In my opinion, we did enough to create chances and sometimes they go in and sometimes they don't."

For a second consecutive game, after losing 1-0 to Western United, City were frustrated by a defensively resolute, deep-lying team.

"We take it as a compliment," Kisnorbo said.

"When there's 11 players behind the ball within the radius of 30 yards from goal, I think that's saying something about the way we play.

"Again, it's going to be hard. I'm not saying it's not and every team plays different but I look at it as a positive.

"We are not going to win every game 20-0. That's reality."

City almost took the lead in the 13th minute when Kosuke Ota deflected Andrew Nabbout's skidding ball into his own net, but it was chalked off for offside after a VAR review.

The game burst to life in the 51st minute when Antonee Burke-Gilroy received a yellow card for a challenge on City captain Scott Jamieson.

The City captain gave Burke-Gilroy some feedback before Perth skipper Bruno Fornaroli burst into the fray to confront Jamieson.

It prompted a brief scuffle involving several players and saw Jamieson and Fornaroli both booked.

Substitute Florin Berenguer sparked City in the 76th minute, forcing when forced an excellent save from Cook with a fierce strike.

In the 83rd minute, Cook brilliantly tipped Good's back-stick header onto the post.

City broke through five minutes later.

Good launched a long ball towards Metcalfe, who nodded it towards the back post, where Atkinson headed home.

Despite the loss Perth coach Richard Garcia delighted in the Glory's resolute performance.

"Very, very pleased. Very gritty, gutsy performance from a bunch of guys who were noticeably fatigued but they dug in for each other," Garcia said.

"That again just reflects on what a good solid unit they are and what a good team they are."

Australian Associated Press