The 69th-ranked Dimitrov turns 20 next month and is the only teen in the top 100. It was his first quarterfinal appearance on the tour.
Despite hitting eight aces, the Bulgarian could not match the steady play of Mayer, who reached his third semifinal of the year.
The last time two German players were in the Munich semifinals was in 1994, when Michael Stich and Bernd Karbacher reached the last four. Kohlschreiber was the last German winner.