Osaka, who is the reigning US, and Australian Open champion has seven career hard-court titles, but has never managed to lift a clay-court trophy.
Muchova, who reached the last four in Melbourne this year, used a single break of serve to claim the opening set against the world number two.
Osaka fell 3-1 behind in the second set but rallied to win the next five games and force a decider.
Muchova however regrouped and broke Osaka early in the third set, and then again for a 5-1 lead, before sealing victory in just under two hours.
