The Germany international has recovered sufficiently from foot surgery to be named in the group travelling to Berlin, although it is likely Sven Ulreich will start the match in goal.
Thomas Muller has also been passed fit after suffering a stomach bug this week, but veteran winger Arjen Robben and defender Jerome Boateng have been ruled out with ongoing muscle problems.
Midfielder Arturo Vidal is also unavailable as he continues his recovery from knee surgery.
Bayern are looking to clinch the domestic double with victory in what will be Jupp Heynckes' final match in charge.
Frankfurt boss Niko Kovac will take over as Bayern head coach on July 1.
Neuer has also been included in Germany's preliminary squad for the World Cup, and may be included in the final 23 if he can prove his fitness.