Louis van Gaal's side missed out on an unprecedented treble for a Bundesliga club of domestic league and Cup and Champions League as they were outplayed by Jose Mourinho's Inter Milan to lose 2-0 at Real Madrid's Bernabeu stadium.
"Of course it's annoying to lose the final after such a fantastic season but Inter played a great match and deserved to win," Bayern chairman Karl-Heinz Rummenigge told the club's website.
"But as after the defeat (in the final) in 1999, now we will put the work in so that we can win the Champions League again within the next two years," added the former Bayern forward and Germany international, who also had a spell playing for Inter in the 1980s
Bayern lost the 1999 final in Barcelona in dramatic fashion to Manchester United after leading for most of the match before going on to beat Valencia on penalties to win in 2001.
Club president Uli Hoeness on Saturday was left thinking about what might have been if Thomas Muller had converted a chance to equalise early in the second half.
Inter goalkeeper Julio Cesar blocked the attacker's shot superbly with his legs and later denied Dutch winger Arjen Robben with an acrobatic save.
"If Muller had put the ball in just after the break maybe something might have clicked," Hoeness said.
"But I said before the final that we have had a fantastic season and we shouldn't let it be spoiled because we lost," he added. "The final is in Munich in 2012 and especially for the younger players there is still a lot to dream for."
Twenty-year-old forward Mueler was barely consolable, saying that Bayern had missed a great chance to add to an already incredible season.
"It's a massive disappointment," he told reporters.
"The squandered chance in the 46th minute was a bitter moment for me," he added. "That's also a reason why I am not feeling so great right now."
