Jupp Heynckes made a number of major changes ahead of the game, a decision that was likely made with one eye firmly on the second leg of their Champions League semi final against Real Madrid on Tuesday.
Young centre back Lars Lukas Mai started once again for Bayern Munich after his appearance against Hannover last week, while a debut was handed to Saturday's goalscorer Niklas Dorsch, as well as Meritan Shabani and Franck Evina.
Frankfurt boss Niko Kovač, who will take over Heynckes at the end of the season, also made a number of changes to his squad this weekend, the most notable of which was leaving star striker Sébastien Haller on the bench.
Bayern Munich took their time at getting a foothold in the game and it was the visitors who offered the first real threat of goal, but an in-form Luka Jović saw his effort easily kept out by Sven Ulreich.
The lively Franck Evina, a 17-year-old who was partnering Sandro Wagner in the Bavarians' attack, then tried his luck from distance but his shot sailed harmlessly wide of Lukáš Hrádecky's far post.
A moment of magic from Wagner forced the visitors' goalkeeper into action minutes later, while Ulreich could only watch as a curling effort from Mijat Gaćinović flew agonisingly wide in the latter stages of an uneventful opening 45 minutes.
But Bayern Munich still had time to take a narrow lead into the break and following some clever work down the right flank, Wagner put the ball on a plate for Niklas Dorsch to tuck the ball into the back of an empty net on his Bundesliga debut.
Eintracht Frankfurt looked to start on the front foot straight after the restart but Luka Jović and Branimir Hrgota were struggling to get on the end of any chances that the visitors were creating.
Thiago Alcântara came close with a long-range effort during one of Bayern's rare bursts forward as the home side looked to get some breathing space over the Eagles. Sandro Wagner then had a clear opportunity to get on the scoresheet but his powerful header was wastefully put wide of the post.
Substitute Niklas Süle got a vital block onto a goal-bound effort from Marco Fabián before his former TSG Hoffenheim teammates, Sebastian Rudy and Sandro Wagner, combined to double their advantage over Frankfurt with just over 10 minutes remaining.
The visitors were finally able to get on the scoresheet through substitute Sébastien Haller but Bayern Munich were able to respond with a brilliant counter attack, with three points confirmed for the hosts thanks to a breakaway goal from Rafinha.
There was even enough time for defender Süle to grab a goal and put the gloss on what was a fairly underwhelming performance from the Bundesliga champions.
The result leaves Frankfurt sitting in seventh place in the Bundesliga table and their place in the Europa League next season could be at risk if they don't return to winning ways sooner rather than later.