UEFA president Michel Platini then presented the trophy to the Mayor of Athens, Nikitas Kaklamanis, so that it might be put on display in and around the city.
They were drawn in Group H alongside AEK Athens of Greece, Anderlecht of Belgium and French team Lille.
Milan won three matches, drew one and lost two to finish top of the group with 10 points and progress to the knockout stage.
However, three minutes into extra time Milan scored when Kaká curled a shot past Celtic goalkeeper Artur Boruc.
Celtic were unable to score the away goal they needed to beat Milan, ensuring the Italians progressed to the quarter finals after a 1–0 aggregate victory.
After six games including four wins, one draw and one defeat, Liverpool finished top of the group with 13 points to qualify for the knockout stage.
The design of the Adidas Finale Athens was based on the widely recognisable UEFA Champions League Starball logo and was blue and white, representing the colours of the Greek national flag.
He was joined by compatriots Carsten Kadach and Volker Wezel as assistant referees, and Florian Meyer as fourth official.
[29] Milan manager Carlo Ancelotti opted to start striker Filippo Inzaghi, who had missed the 2005 final ahead of Hernán Crespo.
Liverpool manager Rafael Benítez opted to field a five-man midfield with Jermaine Pennant and Boudewijn Zenden on the wings, while Steven Gerrard was deployed behind lone striker Dirk Kuyt.
Liverpool fielded five of the players that started the 2005 final: Xabi Alonso, Jamie Carragher, Steve Finnan, Steven Gerrard and John Arne Riise.
Simultaneously, thousands of fans with genuine tickets were refused entry as police closed the entrance to the ground amid fears that allowing any more to enter could have led to a disaster.
[35] The resulting situation became disorderly, with some Liverpool fans attempting to break through checkpoints, set up by the Greek police.
[38] UEFA was itself criticised for poor ticket-checking procedures and for implementing insufficient measures to deal with the large number of fans.
Simon Gass, the British ambassador to Greece, said, "Clearly there was some element of breakdown where those fake tickets appeared to be legitimate – that's something UEFA must look at.
[41] Playing in a 4–2–3–1 formation, Liverpool had the first attack of the match, but Jermaine Pennant could not reach Steven Gerrard's cross-field pass.
Kaká received the ball outside the area and moved to his right before shooting, however Liverpool goalkeeper Pepe Reina saved the shot.
[29] Liverpool continued to exert pressure leading Milan defender Massimo Oddo to mis-read a cross from Pennant, the ball reached Gerrard whose shot went over the goal.
[41] Milan midfielder Gennaro Gattuso was the first player to receive a yellow card, when he was cautioned in the 40th minute for a foul on Alonso.
The subsequent free-kick taken by Andrea Pirlo deflected off the shoulder of Milan striker Filippo Inzaghi, and into the Liverpool goal.
Gerrard capitalised on an error by Gattuso to be one-on-one with Dida, but his shot did not possess enough power to beat the Milan goalkeeper.
[29] In an attempt to bring about an equalising goal, Liverpool manager Rafael Benítez substituted Mascherano for striker Peter Crouch.
With Mascherano substituted, Kaká had the space to pick out a pass to Inzaghi, who took the ball to the side of the Liverpool goalkeeper Reina and rolled it into the net to make the score 2–0 to Milan.
[41] Liverpool managed to pull one goal back in the 88th minute when Kuyt scored with a header after Agger had flicked on Pennant's corner from the left.
This was the first time that the trophy was presented to a winning captain by a UEFA president who had actually played against him in the past; during Michel Platini's final seasons with Juventus, the then-teenager Paolo Maldini was making his professional debut with Milan.
Kaká claimed victory was all the sweeter as a result: "What happened then was strange, just six minutes when we played not so good and we paid for that."
Milan midfielder Gennaro Gattuso echoed his teammates sentiments: "The defeat two years ago will stay me for a lifetime, but this is a different story.
Milan President and owner Silvio Berlusconi was equally delighted about the success, adding that "the fortune we lacked in Istanbul we had with us tonight.
"[47] Liverpool manager Rafael Benítez was disappointed that his team were unable to match their exploits of 2005, when they beat Milan in a penalty shootout.
The match was overshadowed by the death of Sevilla player Antonio Puerta, which raised the possibility that the Super Cup might not go ahead.