The Bavarians' coach says the Londoners' triumph at the Allianz Arena was fully merited as his side failed to take their chances, including a missed Arjen Robben penalty
Thomas Muller gave the Germans the upper hand with less than 10 minutes left at the Allianz Arena, but Didier Drogba equalised moments later for the Blues, before tucking home the winning spot-kick in the penalty shootout.
Nonetheless, Bayern squandered a succession of chances to win the match, including a missed penalty from Arjen Robben in extra time, but Heynckes confessed that the Blues deserved to lift the trophy due to his own side's profligacy in front of goal.
"I think I have to say that we played a good match but we were unlucky on occasions," Heynckes told reporters.
"Our players had a very strong spirit throughout the game and we saw how they played. We attacked from the beginning, and never gave Chelsea the chance to respond.
"Chelsea defended well but we didn't manage to take advantage from our many chances and unfortunately we missed a penalty. We lost our 1-0 lead and Chelsea deserve the title."
Bayern also finished the season second in the Bundesliga and DFB-Pokal.