Atletico managed to beat Fulham in the final in Hamburg, thanks to a extra-time winner from Diego Forlan.
“It was a tough final, in which our people, our fans played a very important part of our success and we are very grateful,” said Flores.
“I am very proud of this players because they have now come full circle and secured a historic title for the club.
“When your in football, you always dream of winning titles and so this is very exciting for us.
“We are aware of what has been achieved, and the people of Madrid deserve to celebrate this.”