It was perfect preparation for Wednesday's Champions League knockout round clash at Arsenal F.C. with Bayern coach Pep Guardiola taking the opportunity to rest four key players: Jerome Boateng, David Alaba, Thiago and Mario Goetze.
Bayern's reserves took full advantage of their chances in a furious first half with Switzerland midfielder Xherdan Shaqiri scoring twice off deflected shots in the first half after defender Dante put Munich ahead in the 19th minute with a glancing header.
Bayern, in fine form after thumping Hamburg SV 5-0 in a German Cup quarter-final match on Wednesday and beating Nuremberg 2-0 last Saturday, shifted down a gear in the second half but still controlled the match.
Claudio Pizarro gave the 71,000 fans in the Allianz Arena a final chance to cheer, scoring after a fine solo run from the left in the 88th minute to put Bayern 16 points clear of Bayer Leverkusen at the top with 59 points from 21 matches.
"Now we've got Arsenal ahead of us and we'll need to have our best possible performance to win," said Guardiola. "We'll have to play at a very high level to advance."
Bayer Leverkusen host fourth placed Schalke in Saturday's late match at 1830 (1730 GMT).
Third-placed Borussia Dortmund downed Eintracht Frankfurt 4-0.
Hamburg SV's woes continued with an eighth successive defeat, 4-2 to Braunschweig.
Hamburg, the only Bundesliga club never to be relegated, fell deeper into the relegation zone in a blunder-filled performance against last-placed Braunschweig, raising further speculation that coach Bert van Marwijk would be sacked.
Germany goalkeeper Rene Adler had an especially dreadful afternoon, with two second-half errors that led to goals. Domi Kumbela came off the bench to score three second half goals for Braunschweig. Last week Hamburg looked at hiring Felix Magath as their coach. Magath was interested but could not reach an agreement with HSV management. On Friday Premier League bottom club Fulham appointed Magath as their manager on an 18-month contract.
Van Marwijk said his side had made unnecessary defensive mistakes. "If you give away goals like that it's hard to do anything."
He brushed aside suggestions that he would be sacked. HSV said the club would review the situation on Saturday night.
"The best medicine would be to win a match or two to regain some confidence," said van Marwijk I'm doing everything I possibly can to help HSV."