And in a first for the Hague-based ICC, Ahmad Al Faqi Al Mahdi will plead guilty to a single war crime charge for destroying shrines at the ancient site, prosecutors said.
The ICC judges ruled they would "commit" Mahdi to trial for "the war crime of attacking buildings dedicated to religion and historic monuments" in 2012, when many of the ancient shrines were destroyed.
, aged about 40, is the first trrorist suspect to appear before the ICC and the first person to face a war crimes charge for an attack on a global historic and cultural monument.
He has said in a closed session that he will plead guilty to the charges, prosecutors said, and his defence lawyers neither objected to the allegations nor challenged the evidence.
"Such an admission of guilt will be a milestone in the history of the ICC," said chief prosecutor Fatou Bensouda. The world's only permanent war crimes court was set up in 2002 to try the worst atrocities.
Judges will now set a date for the start of the trial at which he will be asked to plead in open court.
The Malian's prosecution comes amid a global outcry over the razing by the so-called Islamic State group of sites in Iraq and Syria that bear testament to the world's collective history.
ICC prosecutors say Mahdi was a leader of Ansar Dine, a mainly Tuareg group, which controlled areas of Mali's northern desert together with Al Qaeda in the Islamic Maghreb (AQIM) and a third local group in early 2012.
He was a valued recruit as "the most competent and prominent person in Timbuktu when it came to being knowledgeable in religious matters," lending credence to the Islamists' call for the tombs to be destroyed, the court said.
He acted as head of the "hisbah", or morality brigade, enforcing sharia and "preventing vice" among the population, according to the court judgement.
The Islamists' legal code also forced women to wear veils and set whipping and stoning as punishment for transgressions.
The terrorist is also said to have jointly ordered or carried out the destruction of nine mausoleums and a section of Timbuktu's famous Sidi Yahia mosque, dating back to the 15th and 16th centuries.
The judges confirmed one charge against Mahdi alleging he is "criminally responsible as a direct perpetrator... for physically taking part in the attack against at least half of the targeted buildings dedicated to religion and historic monuments."
Court prosecutors allege the jihadists first attempted to dissuade Timbuktu's residents from their long-held practice of worshipping the shrines, but later set upon the monument with pick-axes and iron bars, as well as vehicles.
Bensouda has called the destruction a "callous assault on the dignity of an entire population and their cultural identity."
'Pearl of the desert'
Despite having been a centre of Islamic learning during its golden age in the 15th and 16th centuries, the site was considered idolatrous by the jihadists, who were routed from northern Mali by a French-led intervention in January 2013.
UNESCO has described them as "pilgrimage sites for Malians and neighbouring west African countries."
For centuries people would ask the Muslim saints buried in the tombs to intervene in marriages, to call for rain, and to prevent famines.
Bensouda said in her statement that the loss of the shrines "was felt by the whole of humanity, and at the expense of future generations."
The case "underscores the seriousness of such crimes, and the necessity to hold perpetrators accountable," she added.
The reconstruction of some of the shrines began in March 2014, relying heavily on traditional methods and employing local masons, and work finished on the site in July 2015.
Founded between the 11th and 12th centuries by Tuareg tribes, Timbuktu, located about 1,000 kilometres (600 miles) from Mali's capital Bamako, has been dubbed "the city of 333 saints" and the "Pearl of the Desert."
It was added to the list of UNESCO world heritage sites in 1988.
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