Douglas Costa grabbed the second goal for Bayern in the 41st minute as the Brazilian connected brilliantly with the cross and powered a header into the back of the net.
Elsewhere title chasing RB Leipzig and Borussia Dortmund both lost ground on Bayern with costly defeats.
It certainly appeared as though Frankfurt were going to take the early 1-0 lead when Branimir Hrgota beat Javi Martinez and rounded Manuel Neuer.
Robert Lewandowski struck twice against Eintracht Frankfurt.
Robert Lewandowski broke the deadlock after 38 minutes at the Allianz Arena, meaning the defending champions have now scored in each of their past 46 competitive matches on home turf.
Again, profligacy was punished, with Alaba darting down the left and teeing up Costa for an emphatic finish and a somersault celebration.
Leipzig had made such a promising start to their first ever top flight campaign and were the true Cinderella story from the first half of the Bundesliga season, but they've seemed to hit a bit of a rut over the past couple of weeks.
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Niko Kovac's men were not cowed into abandoning their attacking intent and the impressive Rebic cut into the box to hit the crossbar before Danny Blum shot wildly over.
Lewandowski passed up a chance to claim the matchball, slotting past the post after Robben played him through.
Bayern's loftier ambitions are set to be realised sooner rather than later.
Ralph Hasenhüttl's men remain in second place in the Bundesliga standings, but Bayern's comfortable 3-0 win over Eintracht Frankfurt gives them a ten point cushion at the top; a gap that looks like it most likely won't be closed down.
Hamburg, in the relegation play-off spot, are now four points away.
The Poland striker scored his second of the game after half-time to reach 100 goals for Bayern in his 136th game. Within their last six Bundesliga matches, they've dropped points on three of those occasions; losses to Borussia Dortmund and Hamburger SV, and the draw against Augsburg.
Seconds after Lewandowski matched his 21-goal tally in Munich, Pierre-Emerick Aubameyang equalized, first playing the ball to Guerreiro with his heel, then running to accept Shinji Kagawa's through ball to score his league-leading 22nd of the season. He headed the ball out wide into space for Thomas Müller.