"I plead guilty," Mahdi said, after being read the charge arising from the 2012 attack on the UNESCO world heritage site when a group of Islamist jihadists swept across Mali's remote north.
Armed with videos, graphics and 360 degree landscapes, ICC prosecutors minutely catalogued before the three judges the destruction in the west African city, dubbed "The Pearl of the Desert."
Aged about 40, Mahdi is also the first Islamist extremist to appear before the tribunal launched in The Hague in 2002 to try the world's worst crimes, and the first facing allegations stemming from the conflict in Mali.
He is accused of "intentionally directing attacks" against nine of Timbuktu's famous mausoleums as well as the Sidi Yahia mosque between June 30 and July 11, 2012.
- City of saints -
Founded between the fifth and the 12th centuries by Tuareg tribes, Timbuktu's very name evokes centuries of history and has also been called "the city of 333 saints" for the number of Muslim sages buried there.
Revered as a centre of Islamic learning during its golden age in the 15th and 16th centuries and a designated UNESCO world heritage site, Timbuktu was considered idolatrous by the jihadists.
Prosecutors on Monday showed shocking images of jihadists smashing down the tombs, pushing down ancient earthen walls and hacking at them with pick-axes while their assault rifles lay nearby.
ICC prosecutors allege Mahdi was a member of Ansar Dine, a mainly ethnic Tuareg movement that in 2012 took control of northeastern Timbuktu along with Al-Qaeda in the Islamic Maghreb (AQIM).
Mahdi, who was then head of the "Hisbah" or the "Manners Brigade", said he was "really sorry" for the damage he had caused.
"I would like to seek the pardon of all the whole people of Timbuktu," he said.
Transferred to the ICC by Niger in 2015, Mahdi was seen as a ruthless jihadist enforcer, fiercely imposing the strictest interpretation of Sharia law.
But vowing that was all in the past, he sought to distance himself from the jihadists describing their acts as "evil."
Dressed in a Western suit with a blue-and-white striped tie instead of his earlier white collarless shirt, he said he hoped "the years I will spend in prison will be a source of purging the evil spirits that had overtaken me".
- Mankind's heritage -
Amid scenes of similar destruction in Iraq and Syria, the ICC prosecutors have said the case is about much more than just stones and walls.
"The heritage of mankind was ransacked," ICC chief prosecutor Fatou Bensouda told the court.
Bensouda told AFP later that it was a "milestone trial", adding Mahdi was cooperating with prosecutors.
"The ICC and my office sent a very strong signal that these kinds of crimes are warcrimes," she added.
The judgement will follow later, but it was revealed that the defence and prosecution have struck a deal under which Mahdi would not appeal a jail term of between nine to 11 years.
The judges warned however the court is not bound by the deal, and he could face up to 30 years imprisonment.
UN Secretary-General Ban Ki-moon said Monday the trial "draws our attention to an increasingly worrying trend of deliberate destruction of cultural heritage in situations of armed conflict."
Such attacks were "a callous assault on the dignity and identity of entire populations," he added.
Critics have also urged the court to investigate allegations of other crimes committed during the Mali conflict, including rape.