Bayern, who face Inter Milan in the Champions League final on May 22, took the lead through Arjen Robben's first half penalty before Ivica Olic doubled their lead in the 51st minute.
Franck Ribery and Bastian Schweinsteiger added two more to cap a memorable domestic season for Bayern.
"I think that we showed an excellent match against a good team," Bayern coach Louis van Gaal told reporters. "I think that was one of the best matches of this season and I think we richly deserved to win."
Bayern, riding a wave of euphoria after their Bundesliga title and their qualification for their first Champions League final in nine years, outplayed Werder for their 15th Cup victory on a cloudy and cold afternoon at the Olympic stadium.
Bremen squandered their biggest chance in the eighth minute when Bayern keeper Hans-Jorg Butt first denied Claudio Pizarro, then Torsten Frings' rebound before Aaron Hunt's third attempt was deflected wide.
SUPERB ROBBEN
Robben should have scored on the half hour mark when he combined beautifully with Thomas Muller but sailed his curled shot just over the bar.
But the winger, enjoying a superb first season at Bayern, got what he wanted in the 35th minute when he thundered in a penalty, awarded for a handball by defender Per Mertesacker.
With their fans chanting "The Tulips from Amsterdam", a nod to Robben and Van Gaal, the Bavarians stepped on the gas.
Olic put the game beyond sluggish Werder when unlucky Germany international Mertesacker cleared only to see his header deflected into the path of the Croat who had no trouble tapping in from close range.
Ribery, in what could be his last match for Bayern as he is suspended for the Champions League final, got on the score sheet when he sprinted to pick up a well-timed van Bommel pass and thread it past Wiese in the 62nd minute.
Frustration boiled over 15 minutes later when captain Frings was sent off with a second booking for a foul on Schweinsteiger. The Bayern midfielder completed the rout eight minutes from time, chesting down a cross to fire home.
"We came into the match good, but we could not get the goal when we needed one to hurt Bayern," said Werder coach Thomas Schaaf.
