Tom Pondeljak struck the winner for Melbourne midway through the second-half, just as ten-man Adelaide United were getting on top.
Before then, referee Matthew Breeze set the tone for a controversial final by sending off Adelaide striker Cristiano inside the opening 15 minutes for an elbow on Melbourne defender Roddy Vargas. Breeze delivered the Brazilian a
direct red card, though replays showed the decision was harsh.
Breeze also handed Danny Allsopp, the Melbourne striker, a direct red in the second-half for what appeared a soft shove on Adelaide defender Robert Cornthwaite. Like the Cristiano dismissal, Allsopp's red card came after Breeze consulted with his assistant. Even at the final whistle, there was a bitter push-and-shove between the two sets of players.
Pondeljak was named Player of the Final and awarded the Joe Marsden medal, he later said: "Adelaide did really tonight and one goal just separated us.
"We deserved this win. We proved we're the best team in the league."
Melbourne captain Kevin Muscat added: "For the past 12 months we've competed for four trophies and won three of them. That's a tribute to the support the players have from all the staff at the club and the fans.
"It was important for us to win here tonight as a way of saying thank-you to the supporters not just for this season, but for the past four years.
"What a team. We showed great mental toughness. You boys deserved this."