The 90,000-euro prize money will pay to sub-title the film in the EU's 23 official languages as well as for the cinema launch.
The movie featured at this year's Cannes film festival in the Un certain regard section.
The other two finalists were Attenberg by Greek director Athina Rachel Tsangari and Play, a Sweden-France-Denmark production.
The prize goes to films that portray values seen as representing European identity or its diverse cultures, or that relate to European Union integration.
Also on Wednesday, the European parliament approved a report on cinema in the digital era that calls for adequate funding to help film producers and distributors, particularly small independent cinemas, to survive the switch to digital projection.