Bayern had set their sights on the Champions League in December 2010 when club president Uli Hoeness mapped out their target of lifting the trophy in their own stadium in 2012.
But 18 months later, that dream turned into an "absolute nightmare".
Bayern started with five youth academy products in the side and despite dominating much of Saturday's game could manage only a 1-1 draw with Chelsea before they were beaten in a penalty shootout.
The German side have now lost two Champions League finals in the last three seasons.
"What happened to us is an absolute nightmare," said Bayern sports director Christian Nerlinger. "The disappointment has gone very deep. It is like a bad movie and it will be very difficult to digest this defeat."
Local boy Thomas Mueller had given the Bavarians an 83rd minute lead but Didier Drogba levelled for Chelsea two minutes from time. Dutchman Arjen Robben's penalty miss in extra time gave Chelsea the chance to snatch the title in the shootout.
Bayern had hoped to ease the pain of a second successive season without a domestic trophy by winning the Champions League, a title that would lift captain Philipp Lahm and Bastian Schweinsteiger on a par with other club greats like Franz Beckenbauer and Gerd Mueller.
Germany captain Lahm had said before the game that without a major title they would never be remembered as a "golden generation."
Lahm and Schweinsteiger, who along with younger Toni Kroos, Mueller, Diego Contento and suspended Holger Badstuber, came through the club's youth ranks, have also got runners-up medals from Euro 2008 and two third place finishes at the 2006 and 2010 World Cups behind them.
Bayern have also played second fiddle to Borussia Dortmund in the Bundesliga in the past two seasons, and lost to them in the German Cup final last week.
Lahm and Schweinsteiger, who missed his penalty in the shootout, hung their heads as they left the stadium and did not utter a word to waiting reporters.
They know that at 28 and 27 respectively time is gradually running out for that elusive major trophy.
While club success will have to wait, they will get another shot at silverware next month when they lead Germany into battle at Euro 2012 with fellow internationals Badstuber, Mueller and Kroos.
"We will build the boys up. With us they can still win a title," said Germany team manager Oliver Bierhoff.