Defending champion City, smarting from a first defeat of the A-League season at the hands of Western United, dominated the game but Glory goalkeeper Cameron Cook denied them time and again.

Atkinson finally broke the deadlock in the 88th minute, nodding home from close range after Connor Metcalfe timed his run to perfection and headed into the substitute's path.

Melbourne had 23 attempts and thought they had opened the scoring in the first half, but Andrew Nabbout's deflected strike was ruled out for offside.

While Melbourne will point to its domination of the game, Atkinson's winner was a cruel blow for Cook, who made six saves.

Victory for Patrick Kisnorbo's side moved them up to second place, with Perth sitting into sixth spot after four matches.