Bayern had the majority of the ball in the first period, but a strike from Fernando Torres after eight minutes ensured that the Premier League outfit entered the break ahead.
Bayern were level in the early stages of the second half courtesy of a strike from Franck Ribery, but that was how it ended as the match entered extra time.
Here, Sports Mole dissects the 90 minutes of action between the two sides.
On target: 19
On target: 9
Was the result fair?
Conceding in the last kick of the game was tough on Chelsea, but it is difficult to argue that Bayern did not deserve to claim the trophy this evening. They dominated the possession throughout the 120 minutes of football, registering 35 attempts, 19 of which were on target. Chelsea must be credited for their defending, but Bayern never gave up and you always felt that they would have enough to claw it back in the latter stages.
Despite dominating possession throughout the evening, Bayern did struggle to create clear opportunities, especially in the second period. That, of course, was not the case when Chelsea were reduced to 10 men, but the German champions will have to be more clinical if they are to enjoy more success this season. However, there is no question that they will once more be the team to beat in the Champions League.
It was a spirited performance from Chelsea, who somehow managed to move ahead in extra time despite being reduced to 10 men. On another evening, they might have been out of the game by that point, but the likes of Gary Cahill and Ashley Cole were terrific in defence. It was also a good night for Torres, who found the back of the net in spectacular fashion after eight minutes. In the end, however, they just did not do enough to deserve to claim the trophy.
Sports Mole's man of the match
Petr Cech: The simple fact of the matter is that Chelsea would not have been in a position to win on penalties if they did not have the Czech Republic goalkeeper between the sticks. The experienced keeper was called upon to make a number of saves in the latter stages, including a point-blank stop from Mario Mandzukic, before he tipped a Ribery free kick wide of the post.
Biggest gaffe of the match
Unfortunately, this has to be given to Ramires. The Brazilian put in a tireless performance for his side, especially in the first period, but he was given his marching orders for a horrendous challenge on Mario Gotze in the second period. Not only was it a reckless tackle that could have caused the German serious discomfort, but it also put his side in all sorts of problems.
Jonas Eriksson can be pleased with his display this evening. The Swede hardly featured in the first period as he allowed the two sides to play without too many stoppages, but he was called into action in the second period. The 39-year-old also got the sending off decision spot on, although he might have produced a straight red rather than a second yellow. Neither manager will have had too many complaints about his performance in Prague.
Bayern: Bayern will attempt to return to winning ways in the Bundesliga when they welcome Hannover 96 on September 14.
Chelsea: The Blues also return to domestic action on September 14 against Everton at Goodison Park.