The glass pane, which was 150 cm long and 30 cm wide, smashed through the car's windscreen, but luckily the 26-year-old driver remained uninjured, Die Welt reports.
The pane was apparently not an essential part of the structure of the building but was there for decorative purposes.
The Bahntower, which is the headquarters of rail operator Deutsche Bahn (DB) is 103 meters tall and was built between 1996 and 2000 on the former border line between east and west Berlin.
In 2005 a similar incident occurred when a window pane fell around 30 meters from the building onto the pavement below.
DB say that they are not responsible for the upkeep of the building and, despite the name, are only the tenant.
Upkeep of the outer facade is carried out by an external management firm.
Local authorities “will take all necessary measures to ensure that this type of event does not happen again,” a spokesperson for the capital's central Mitte district told Die Welt.