Archie Thompson's extra-time winner guided Melbourne Victory into the Hyundai A-League semi-finals after a dramatic and highly controversial 2-1 triumph over Perth Glory.

Archie Thompson's extra-time winner guided Melbourne Victory into the A-League semi-finals after a dramatic and highly controversial 2-1 triumph over Perth Glory at Etihad Stadium on Friday night.

Perth Glory looked to have booked a date with the Western Sydney Wanderers in next Friday's preliminary final until two minutes of mayhem turned the game on its head.

A penalty at either end and a red card to Glory defender Steve Pantelidis swung the momentum entirely in Victory's favour.

After twice spurning golden opportunities to put the contest to bed, the returning Shane Smeltz crashed an 88th-minute penalty into the crossbar when a conversion would have made it 2-0 for his side after Ryo Nagai put the Glory ahead in the first half.

Less than two minutes later substitute Andrew Nabbout was awarded a controversial penalty and Steve Pantelidis then received his second yellow as referee Jarred Gillet pointed to the spot.

Mark Milligan held his nerve to cushion home the penalty and the shell-shocked Glory would go a goal behind when Marco Rojas' brilliant cross found Thompson's stooping head and the back of the net four minutes into extra-time.

Soon after, Glory attacker Nagai saw his penalty claim waived away, and the Victory wasted two golden chances for a third in the dying embers of a breathless contest at Etihad Stadium.

For much of the match, it appeared double-title winning coach Ange Postecoglou's hopes of a fairy-tale three-peat were no more than a pipedream.

Nagai deservedly put the visitors ahead on 15 minutes, and if it were not for Smeltz's trio of second-half misses, Glory's title hopes would be alive and well.

Smeltz was deemed fit to start, albeit with a headband covering a 15-stitch gash, as Liam Miller also returned.

Marshalled by captain Adrian Leijer, the Victory defence had kept a clean sheet only once in their past 10 A-League games.

And Perth were clearly given direct orders to exploit that inexperience.

Youthful full-backs Geria and Galloway were routinely targeted down the flanks by dynamic duo Adrian Zahra and Nagai.

Zahra was the first to blaze over on 11 minutes when played through, but the goal was soon to come when Scott Jamieson - charged with the task of shutting down Victory's prime threat Marco Rojas - overlapped down the left.

His pin-point cross deceived Leijer and caught goalkeeper Nathan Coe in no man's land, allowing Nagai to nonchalantly chest the ball into the empty net.

With Rojas kept quiet, the majority of Victory's attacks were coming down the left through Galloway, while Perth's midfield trio - Jacob Burns, Liam Miller and Matias Cordoba - were mopping up everything in the centre of the park.

Jamieson rocked Billy Celeski with a crunching challenge that drew the first yellow card and no sooner was he up, Rojas pick-pocketed him and set off one of his signature mazy runs.

The crafty New Zealand international cut inboard and put the ball on a platter for Broxham, only for the midfielder's hot to be deflected wide.

The deflection went unchecked by the referee to the growing frustration of the home crowd, who were forced to wait until the 35thminute for Victory to create their first genuine chance.

Perhaps belatedly, Flores was introduced on 49 minutes for Geria, prompting Broxham to shift to right-back as the Argentine joined Thompson in attack.

Smeltz received a dream ball from Miller, and, with acres of space cut back inside to go one-on-one with the keeper only for Coe to smother his attempt.

A second Glory goal could well have put the match to bed, but instead it was Flores testing Vukovic at the other end moments later with a header that looped onto the roof of the net.

Perth continued to defend manfully and waited patiently to break forward.

Again, Smeltz was the target as he curled Nagai's teasing cross over the bar with less than 20 minutes to play.

And, he was to prove just as unlucky from the spot as Victory buried their corresponding penalty and ensured they will fight another day against the Mariners next Sunday courtesy of Thompson's extra-time winner.

Bet365.com Man of the Match: Ryo Nagai The Japanese winger was a constant menace for Glory. He's not the finished product but was always willing to go forward.

Melbourne Victory 2 (Milligan 90, Thompson 94) Perth Glory 1 (Nagai 15)

Crowd: 22,902 @ Etihad Stadium