The Serge Gnabry sat out the clash with a bruised back, as Ivan Perisic was brought into the Bayern attack.
Bayern, who hammered Frankfurt in the league three weeks ago, were quick on the attack as Thomas Muller forced a goal-line clearance of Dominik Kohr following a Joshua Kimmich corner.
The opener eventually arrived when a cutback from Robert Lewandowski found Thomas Muller who in-turn picked out Ivan Perisic to complete the move with a simple header after 15 minutes.
It should've been two for the home side just before the half-hour mark when a cross from Alphonso Davies found Kingsley Coman at the back post, but the Frenchman failed to capitalise.
Eintracht began the second half with a lot more urgency but the reigning champions almost had a second goal after Coman combined with Kimmich who forced Kevin Trapp to a smart save on 58 minutes.
Eintracht were level with just over 20 minutes remaining after Daichi Kamada's scuffed ball in the area fell nicely to substitute Danny da Costa, who needed no second invitation.
The Bavarians quickly restored parity when unselfishness from Kimmich resulted in a cutback for Lewandowski to slam home from six yards after the 74th minute.
Bayern were pushed to the edge in the remaining minutes by their counterparts, but held on to reign victorious.
Saarbrücken 0-3 Bayer Leverkusen