The ruling is the first of its kind, and supporters hope it sends a warning that destroying such sites will not go unpunished.
It was the first such case before the international court in The Hague to focus on cultural destruction as a war crime.
After a brief trial in August, it found Ahmad al-Faqi al-Mahdi guilty of directing attacks on Timbuktu during the militant takeover of northern Mali in 2012.
Between June and July of that year, 10 of the most important and well-known sites at the UNESCO world heritage site were attacked and destroyed.
Ahmad al-Faqi al-Mahdi pleaded guilty to the single war-crimes charge of "intentionally directing" attacks on nine of Timbuktu's mausoleums and the centuries-old door of the city's Sidi Yahia mosque.
Presiding judge Raul Pangalangan handed down the sentence.
"Mr al-Mahdi, the crime which you have been convicted of is of significant gravity. This said, the Chamber has found no aggravating circumstances and five mitigating circumstances: namely, your admission of guilt, your cooperation with the prosecution, the remorse and empathy you have expressed for the victims, your initial reluctance to commit the crime, and the steps you took to limit the damage cost -- and even, of limited importance, your good behaviour in detention despite your family situation. Taking into account all these factors, the Chamber unanimously sentences you to nine years of imprisonment."
Ahmad al-Faqi al-Mahdi asked for forgiveness.
He says he was swept up in what he describes as an "evil wave" by al-Qaeda and the Tuareg-dominated Ansar Dine group that briefly seized control of the ancient sites.
The International Federation For Human Rights' Carrie Comer says the sentence sends a strong message.
"Continuing to give a nine-year sentence in spite of those mitigating circumstances is actually quite a strong, deterrent message,
saying, 'We do take these crimes seriously.' They have an impact on victims not only in the immediate vicinity, but, really, in the international community as a whole, and, hopefully, this will provide some sort of deterrence."
Tuareg tribes founded Timbuktu between the fifth and 12th centuries.
It has been dubbed The City of 333 Saints for the number of Muslim sages buried there.
Although revered as a centre of Islamic learning during its golden age in the 15th and 16th centuries, militants who swept across Mali's remote north in 2012 considered it idolatrous.
UNESCO says about 55 places around the world are on its list of endangered cultural heritage sites.
Director general Irina Bokova has welcomed the verdict.
"My first feeling, of course, is of justice. It is that impunity should not be the answer to the destruction of cultural heritage. And I would emphasise cultural heritage that belongs to the whole of humanity, because we are speaking about heritage that belongs to the list of world-heritage sites. On the other side, I think it is justice also for the local people, for the local communities, in Timbuktu."
The international court's landmark verdict is also its first arising out of the conflict in Mali.
