In a summary of their verdict, the judges said Al Hassan Ag Abdoul Aziz played an important role in Ansar Dine, an Islamic extremist group with links to al-Qaeda that 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 on Wednesday.
Al Hassan has pleaded not guilty to all charges, but has not denied he was a member of Ansar Dine.
His lawyers have argued he was trying to maintain order in a chaotic situation after the rebel takeover of Timbuktu.
Clad in a traditional West African yellow robe and white head dress, Al Hassan, 47, showed no emotion when the court also convicted him of religious persecution and the war crimes of mutilation and participating in sham trials.
Prosecutors had charged Al Hassan with a number of gender-based crimes, saying the Islamic police terrorised the women of Timbuktu, who were subjected to rape, forced marriages and sexual slavery.
While judges said rape and forced marriages did take place in Timbuktu they found Al Hassan bore no responsibility for such crimes.
Prosecutors have 30 days from the judgment to file an appeal.
Al Hassan's sentence will be determined at a later date after another round of hearings. The ICC can impose a maximum sentence of life in prison.
Al Qaeda-linked fighters of Ansar Dine also used pick-axes, shovels and hammers to shatter earthen tombs and centuries-old shrines reflecting Timbuktu's Sufi version of Islam in what is known as the "City of 333 Saints".
But judges found that Al Hassan had no role in the destruction and acquitted him for charges related to the attacks.
Last Friday the ICC unsealed an arrest warrant for the alleged leader of Ansar Dine, Iyad Ag Ghaly, also known as Abou Fadl.
Another Islamist rebel was given a nine-year sentence by the ICC in 2016 after pleading guilty to participating in destruction of Timbuktu's religious monuments.
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.
