"It's crazy. We consider this as attempted murder," said shocked Hertha team manager Michael Preetz, who revealed that only the driver had been in the bus at the time and had miraculously escaped unscathed.
"Our driver was going from the hotel to the train station at Bielefeld to collect the team," explained Preetz.
"An unidentified person on a motorbike fired at the bus," he said, adding that "the type of firearm used has not yet been determined".
A photo posted by the club on Twitter showed the impact of the bullet which smashed a hole in the windscreen at the level of the driver's head.
Police told SID, an AFP subsidiary, that an investigation was underway, as second-division Bielefeld condemned the attack.
"We're shocked by the attack on the Hertha Berlin bus. Fortunately no Berlin colleague was injured," the club from North Rhine-Westphalia region of western Germany said on Twitter.
The incident overshadowed the first round of matches where Bayern Munich got their Cup campaign off to a 3-1 winning start over amateur fifth-division side Noettingen as Bundesliga rivals Hamburg fell at the first hurdle for the second consecutive year.