The Japanese winger cleverly chested home a Scott Jamieson cross from the left which Victory goalkeeper Nathan Coe badly misjudged.
From then on the Victory poked and prodded but were unable to penetrate a disciplined and committed Glory defensive effort.
But after the Glory appeared in control and on the way to the next stage of finals, all hell broke loose with two late penalties - with vastly different results.
Firstly Gillett penalised Victory's Mark Milligan for bringing down Jamieson in the box in the 87th minute.
But Glory's Shane Smeltz missed the penalty which could have put his side two-up and sealed a win.
Then in the last minute of normal time, Gillett adjudged Glory defender Steve Pantelidis to have pulled Victory attacker Andrew Nabbout's shoulder, awarded a spot-kick, and sent Pantelidis off.
Milligan slotted home the equaliser to send the match to extra-time.
But with the Glory shell-shocked, the Victory struck just four minutes into extra-time when Archie Thompson headed home from close range after a Marco Rojas cross.
With both sides out on their feet, the Glory also had a penalty shout turned down in the second period of extra-time, when Nagai fell in the box.
Glory coach Alistair Edwards admitted there were ``a few angry boys'' in the change-room post-match as a result of the Pantelidis penalty - in which Nabbout appeared to handball prior to the contact being made.
But Edwards refused to use it as an excuse for his side's loss, believing they should have put away their own penalty and other chances in normal time.
"I feel immense pride in the boys, the way they performed tonight, the way they performed over the last eight games to go from bottom of the table to playing in such a marvellous final,'' Edwards said.
"I'm disappointed because we should have won the game ... while the boys are pretty angry at the moment, I'm really proud of them.
"We should have won the game. We should have scored the penalty. We should have converted a few more chances.
"But it's onwards and upwards, and we push through the disappointment.''
Postecoglou, whose Roar teams won two grand finals with the latest of late shows, admitted his side's win wasn't pretty but didn't believe they were lucky to win.
"In finals games, the most important thing is that you've got your nose in front - whichever way you can. And we got our nose in front today,'' he said.
"We've done as we've done a fair bit this year, and conceded a soft goal for no reason.
"But you keep going to the final whistle and the opportunity will come, and sometimes it does come in the final minute of a game.''
-AAP
