The autopsy carried out on the girl enabled investigators to "determine without a doubt that this was a homicide," police spokesman Eberhard Wagner said.
Police did not release further information about the circumstances of the death due to the ongoing investigation.
Walkers came upon the still-clothed body of the girl in a forest creek near the town of Zella-Mehlis in southern Thuringia. The body's location was about 1.5 kilometres from where the girl had lived with her mother.
The girl had been missing since Friday evening when she failed to return from school.
On Saturday evening, a vigil was held in the town in which some 700 people took part, police said.