Ahmad al-Faqi al-Mahdi admitted to leading rebel forces who destroyed historic mausoleums at the world heritage site in Mali in 2012.
Judges at the court in The Hague found he had shown “remorse and empathy” for the crime.
It is the first sentence based on cultural destruction as a war crime.
It is also the first time a suspected Islamist militant has stood trial at the ICC.
Mahdi – described as a “religious scholar” in court documents – led rebels who used pickaxes and crowbars to destroy nine of Timbuktu’s mausoleums and the centuries-old door of the city’s Sidi Yahia mosque.
The court found he not only offered “logistical and moral support” for the attacks, but also took part in the physical destruction of at least five out of the 10 buildings.
However, Mahdi had at first advised rebel leaders not to attack the shrines.
Admitting to the charges last month, Mahdi claimed he had been swept up in “an evil wave”.
Pleading guilty, he said: “I am really sorry, I am really remorseful, and I regret all the damage that my actions have caused.
“I would like to give a piece of advice to all Muslims in the world, not to get involved in the same acts I got involved in, because they are not going to lead to any good for humanity,” he added.
Wearing a grey suit, striped tie and spectacles, there was little sign of the violent jihadist responsible for destroying these treasured shrines.
Ahmad al-Faqi al-Mahdi was a member of a group with links to al-Qaeda and the leader of the morality police (a religious vice squad operating in Timbuktu during the rebel occupation).
According to the judge, he wrote a sermon dedicated to the destruction, gave instruction and tools to complete the operation. His confession, a well-considered apology and apparent willingness to co-operate with the court contributed to the nine year sentence.