The Teddy, now in its 20th year, goes to the film in the festival line-up that does the most to advance gay and lesbian rights. It includes a $3,570 cash prize and is awarded by a nine-member jury.
The film, which was featured in the childrens film section of Berlinale, tells the story of a boy torn between his love for his criminal father and his attraction to the honest policeman who befriends him.
The Teddy for best documentary, which also includes a 3,000-euro prize, went to French director Olivier Meyrou for "Beyond Hatred" (Au-dela de la haine) about three skinheads accused of beating a gay man to death.
The prizes were awarded at a gala ceremony attended by Berlins gay Mayor Klaus Wowereit and festival director Dieter Kosslick.
Previous Teddy winners include US filmmaker Gus Van Sant of "Drugstore Cowboy" fame and French director Francois Ozon ("Swimming Pool").
The 56th Berlinale will award the festivals main prizes including the Golden Bear for best film Saturday night.