The 44-year-old, who won the prestigious trophy with Dortmund in 1997, criticised the English side's playing style in their penalty shootout victory, which came after the Blues and the Bavarians played to a 1-1 draw after 120 minutes.
"If this is the future of football, then it's a catastrophe," he said after the game.
"It's unfair that those with such a playing style as Chelsea can win titles."
Bayern squandered several chances, including a penalty, over the course of the 120 minutes of play, but could not capitalise as Thomas Muller's late opener was canceled out by Didier Drogba.
In the eventual shootout, Chelsea came out the victors, claiming their first-ever Champions League trophy.