Gunshots and car alarms could be heard as fans attacked cars and smashed nearby shop windows.
Many Bosnian Muslims back Turkey in international competitions for historical and cultural reasons that date back to the five centuries of Ottoman rule in the Balkans, while Croats regard the Croatian national team as their own.
"Dozens of people were admitted to hospital, including four police officers of whome one with serious injuries," a local doctor said.
Mostar has a history of football-related violence. The southern Bosnian city has roughly an equal number of Croats and Muslims, who were enemies during a 1993-1994 conflict but later became allies against Bosnian Serbs.