In a summary of their verdict, judges said Al Hassan Ag Abdoul Aziz played an important role in the Ansar Dine Islamist group which took the city on the fringe of the Sahara desert in 2012 and tried to impose sharia Islamic law.
Local inhabitants testified that he was considered a key player within the Islamic police force who could issue orders and police officers would carry them out.
"Al Hassan has been found guilty by majority decision of war crimes and crimes against humanity, including torture, cruel treatment and outrages upon personal dignity, for the public flogging of 13 members of the population" of Timbuktu, Presiding judge Antoine Kesia-Mbe Mindua said.
The sentence Al Hassan will receive will be determined at a later date after another round of hearings. He faces a maximum sentence of life in prison.
The ICC, the world's only permanent war crimes tribunal, has been examining events in Mali since 2012. French and Malian troops pushed the rebels back the following year.