The emergency brake was pulled on a train containing 900 football fans just before it entered the station near Frankfurt's Commerzbank-Arena. The Frankfurt fans then attacked the train, while further fights broke out between the station and the stadium.
Fans of both clubs threw bottles at one another, while the police said they surrounded and kettled some 100 Frankfurt fans to try to stem the violence.
The police had several hundred officers at the scene who attempted to guide the two sets of fans to the stadium separately. A police spokesman said that fights of this scale were unusual.
The train was heavily damaged, with several windows smashed, and the line between Mainz and Frankfurt had to be suspended for 90 minutes.
The so-called "Ultras" had already made their presence felt in the morning in the Frankfurt inner city, where around 400 hooligans threw fireworks at policemen and passers-by.