The International Criminal Court ordered victims be paid "individual, collective and symbolic" reparations, ICC judge Raul Pangalangan said.
But the judges at the Hague-based tribunal recognised that Ahmad al-Faqi al-Mahdi was penniless, saying it was up to the Trust Fund for Victims (TFV) - set up to implement the judge's decisions - to decide how the outstanding amount will have to be paid.
The judges further ordered that the Malian state as well as the international community be compensated with a symbolic amount of one euro for the damages suffered.
Jihadists used pickaxes and bulldozers against nine mausoleums and the centuries-old door of the Sidi Yahya mosque, built during a golden age of Islam, after a jihadist takeover in northen Mali in 2012.
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Al-Mahdi was jailed for nine years in 2016 after he pleaded guilty to directing attacks on the UNESCO world heritage site and apologised to the Timbuktu community.
Timbuktu, founded by Tuareg tribes between the fifth and 12th centuries, has been nicknamed "the city of 333 saints," referring to the number of Muslim sages buried there.