Sedat Ergin, who was in Bonn to receive the award, was charged last December with insulting Turkish President Recep Tayyip Erdogan in a headline on the newspaper's website.
If found guilty, he faces up to five years and four months in prison. His trial has not yet begun.
"Hurriyet is one of the biggest and one of the last independent media outlets, a torch of liberty and one of the last bastions of freedom of opinion in Turkey," said Kai Diekmann, editor-in-chief of Bild, Germany's biggest-selling daily, in remarks made at the award ceremony.
One of Turkey's most popular dailies, Hurriyet mixes mainstream news coverage that generally toes the government line with popular columnists known for their opposition to Erdogan, such as the very prominent Ahmet Hakan.
The recent hiring of prominent pro-Erdogan columnist Abdulkadir Selvi also brought a different voice into the newspaper.
Concerns have been rising about press freedoms in Turkey under Erdogan, with thousands of people prosecuted for insulting the president and two top journalists from the opposition Cumhuriyet daily on trial for revealing state secrets.
The award was presented as German and Turkish ties sank to a low over the Bundestag's decision to recognise World War I-era mass killings of Armenians by Ottoman forces as a genocide.