With Perth Glory coach Kenny Lowe banished to the stands over a clash with the referee, Andy Keogh scored a hat-trick to topple Melbourne City 3-2 at AAMI Park.

Twice Keogh put Perth ahead from set-pieces in Friday night’s A-League match but City found replies either side of half-time through Bruno Fornaroli’s penalty and Fernando Brandan.

Five minutes from time, the Irishman was the hero and City pair Josh Rose and Dean Bouzanis the villains after they conspired to hand Keogh his third.

With Bouzanis well off his line, Rose’s defensive header fell straight to Keogh, who lobbed the goalkeeper to secure a result that puts Perth on top of the competition.

Glory yielded a majority of possession but were worthy winners after arriving in Melbourne with a better intent than their hosts.

The Dino Djulbic tackle on Bruno Fornarelli that led to a controversial penalty.

From the early exchanges it became clear the Glory’s counter-attacking game was going to cause City more problems than John van ‘t Schip’s side encountered in last weekend’s derby stroll.

Sure enough, on seven minutes Perth took the lead with a effort straight from Lowe’s little black book of set plays.

Neil Kilkenny’s barge on young centre-back Alex Grant drew a free kick in the middle of the park.

Nebojsa Marinkovic lofted the ball into the path of Chris Harold, who cut-back for Keogh to tap in.

City were asleep for the goal and looked groggy for most of the half.

But Fornaroli fashioned a way for City to get back in the contest, wriggling free in the box and catching the leg of Dino Djulbic for a penalty.

The Uruguayan made no mistake from the spot, giving City parity at the break.

Djulbic, man of the match Rostyn Griffiths and Lowe were enraged, confronting referee Alan Milliner at half-time, with the coach given his marching orders for the incident.

He was banging the glass of his corporate box in celebration just four minutes after play restarted, when Glory again scored from a dead ball.

Glory coach Kenny Lowe had words with the officials at half time (above), ensuring he watched the second half from the stands (below).

From Marinkovic’s corner, Luke Brattan cleared Djulbic’s header off the line and back to the giant defender.

At the second effort, Djulbic headed to Keogh, whose header was fumbled over the line by Bouzanis.

City roared back, equalising through Brandan after he was played in by the otherwise quiet Tim Cahill.

The home side were finishing stronger until the late howler gave Perth their first win over City in Melbourne since January 2012.

Lowe said his side deserved it. “Coming here against probably the best team in the league into the lion’s den … we deserve credit to come here and score three goals – three quality goals – and I think Andy Keogh possibly could have had another three.

Lowe suggested Keogh’s late substitution wasn’t injury-related and “he just wanted a clap”.

Worse for van ‘t Schip, Nicolas Colazo didn’t play with an ear infection, Bruce Kamau was substituted early with concussion and Luke Brattan limped out the match.

All three are in doubt for their FFA Cup semi-final with Melbourne Victory on Tuesday.

“Tonight the boys obviously tried but the performance was not good,” he said.

“We lost the ball too early and made the opponent strong and dangerous.”