Dortmund in the first all-German final in Europe's top club competition and wiped away bitter Bayern memories of showpiece defeats in 2010 and 2012.
The Bundesliga champions can complete a German treble in the German Cup final against VfB Stuttgart next Saturday and such is the strength of their overall setup, further success is fully expected in the next few seasons.
Bayern coach Jupp Heynckes, 68, is retiring at the end of the season having become only the fourth manager to have lifted the European Cup with two different clubs having also won with Real Madrid in 1998. Read: Match-winner Arjen Robben breaks finals hoodoo
Bayern Munich's players and staff celebrate with the trophy on the pitch after their victory in the UEFA Champions League final football match between Borussia Dortmund and Bayern Munich at Wembley Stadium in London. AFP
He gives way to ultra successful former Barcelona boss Pep Guardiola and with Dortmund's Germany midfielder Mario Goetze already signed up for next term and their striker Robert Lewandowski also eyed, Bayern's confidence can only skyrocket.
"Bayern will have to prove that they can continue to achieve these things but it is quite possible a new era might have begun for Bayern Munich," Heynckes told a news conference.
Munich parties as Dortmund mourns
Bayern Munich fans celebrated long into the night after their team's 2-1 Champions League triumph over Dortmund at Wembley on Saturday ensured two defeats in the previous three finals were quickly forgotten.
More than 40,000 Bayern fans erupted in delirious joy when Arjen Robben scored the 89th minute winner as they watched the match on a chilly, wet night at a special public viewing event set up on Munich's Oktoberfest grounds. Read: Dortmund rues missing golden opportunity to win Champions League
Another 50,000 Bayern supporters watching on video screens at Bayern Munich's Allianz Arena were finally able to celebrate after the Dutch forward rescued them from the prospect of another heartbreaking defeat on Europe's biggest stage.
Many stormed the vacant pitch to proclaim the famous victory and tear up sods of turf as souvenirs.
Performers dressed as medieval soldiers entertain during the opening ceremony of the UEFA Champions League final football match between Borussia Dortmund and Bayern Munich at Wembley Stadium in London. AFP
"It's superb and I feel so relieved," said Marco Goering, who had joined thousands of fans on Munich's fashionable Leopoldstrasse in a spontaneous midnight rally.
"It's an overwhelming feeling. Three finals in four years. It's a fantastic feeling to see how the fans are going crazy here, a great feeling." Read: Last-gasp Robben gives Bayern fifth Euro crown
Singing, dancing and slapping each other on the back, many fans offered their own rendition of the Queen song "We Are The Champions" as well as traditional fan chants praising Bayern.
The mood was entirely different 600-km to the north in Dortmund, a former mining town about as far away from the glitzy and cosmopolitan world of Munich that you can get in a country where opinion was divided on who was the popular choice in the all-German final.
The match began well for the thousands of Dortmund fans packed into the Friedensplatz square in their black and yellow jerseys after the team dominated their loathed opponents for much of the first half.
Joy turned to despair when Munich scored after an hour before a deafening roar greeted Dortmund's equaliser in the 68th minute, reviving memories of Bayern's squandering of a 1-0 lead in last year's final before losing on penalties to Chelsea.
However, Robben's late intervention did nothing more than to leave the crowd in stunned silence.
"It's all crap and I don't know what to say," said Dortmund fan Daniel Ruetting as others nearby wept openly. "It's time to go home and sleep over it. There's always next year."
Borussia Dortmund's players react after their defeat in the UEFA Champions League final football match between Borussia Dortmund and Bayern Munich at Wembley Stadium in London. AFP
A year ago, the Bavarians were distraught after losing the final to Chelsea from a winning position on their home ground but after weathering an early Dortmund storm at Wembley, their experience shone though.
"We didn't resign ourselves to our fate (after the Chelsea defeat)," Heynckes said. "We upped the ante and tried even harder. You have seen the result."
Bayern may not be as youthful as Dortmund, leaving Guardiola and the board with work ahead of them to renew the squad, but a generation of top players including Robben, Franck Ribery, Bastian Schweinsteiger and Philipp Lahm have now finally won the ultimate club prize.
Bayern Munich's Dutch midfielder Arjen Robben celebrates at the final whistle after their victory in the UEFA Champions League final football match between Borussia Dortmund and Bayern Munich at Wembley Stadium in London. AFP
"The team is in the right age group and we've got rosy times in front of us. We want to win the treble and as far as I'm concerned this can keep going next year too," right back Lahm said.
Bayern, winners of five European Cups dating back to their 1970s domination when they won three straight titles, have also achieved renewed success despite changing their main central striker almost every season.
Luca Toni, Ivica Olic and Mario Gomez have all been eased out, although Gomez is still at the club, and incumbent Mario Mandzukic will be nervously looking over his shoulder despite an excellent first season and the 60th minute opener on Saturday.
The Croatian will be well aware of Lewandowski's attributes and if the Pole does head to Bayern, the competition for places will only make them an even scarier prospect.
Bayern Munich's Croatian striker Mario Mandzukic scores the opening goal of the UEFA Champions League final football match between Borussia Dortmund and Bayern Munich at Wembley Stadium in London. AFP
For Dortmund, losing the final and possibly two of their best players to much richer rivals Bayern cannot take away the feeling of pride after they wowed the Champions League this season with a series of exciting attacking displays.
Their ability to regenerate after selling key players after their Bundesliga titles in 2011 and 2012 means they too, could remain a force as Germany looks to supplant Spain and England as Europe's best league.
Dortmund's madcap coach Juergen Klopp, whose side levelled on 68 minutes thorough an Ilkay Guendogan penalty, was impressed with his side's energetic display.
"Yes the quality struck me and I'm sure next season we'll have more quality," he said.