Late second-half strikes from Thomas Muller and Didier Drogba eventually saw the final decided by penalties, which were settled by the Ivorian.
Didier Drogba's winning spot kick in a penalty shootout ensured Roman Abramovich's nine-year long dream of triumphing in Europe's elite club competition finally came true.
A tense final was witnessed in Germany, where much of the first half saw Chelsea deploy similar tactics to those that were on show against Barcelona in the semifinal stage of the competition.
However, the game opened up after the break as both teams went in search of the winning goal, and Bayern thought it had found it with just nine minutes left on the clock through Thomas Muller.
The trophy appeared to be staying in Bavaria, but Drogba's header at the death meant the final would be taken into extra time in the most dramatic of circumstances.
The added time still could not determine who would triumph, meaning penalties were needed to decide wh which side would win for a 10th time in a European cup final.
Bastian Schweinsteiger's missed spot kick gave Drogba the chance to banish his side's demons of the 2008 final against Manchester United, which he duly took to crown Chelsea as European champion four years on.
For Bayern, the club has now finished runner-up in two of the previous three Champions League campaigns, and has ended the season without a trophy after also previously losing out in the Bundesliga and the DFB-Pokal.
Meanwhile for Chelsea, interim boss Roberto Di Matteo has now lifted the FA Cup and the Champions League during his brief reign at Stamford Bridge, while also securing top-level European football for the Blues at the expense of Tottenham next season.
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