Hertha published a photograph of the damaged bus windscreen on their website and said driver Stefan Behrendt was unhurt.
"We are deeply shocked and hope that the perpetrators will be caught. Luckily our bus driver got away with just a fright," Hertha sporting director Michael Preetz said.
Hertha are due to play at second tier Arminia Bielefeld in the Cup first round on Monday.
"We are shocked about this attack on the team bus of Hertha. Luckily the Berlin colleague was not injured," Bielefeld said on Twitter.
Such incidents are very rare in German football but violence occasionally occurs.
(Writing by Mark Meadows, editing by Ed Osmond)
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