Still, there was celebration among the thousands of Timbuktu residents who fled the city rather than live under strict and pitiless Islamic rule and the dire poverty that worsened after the tourist industry was destroyed.
"In the heart of people from northern Mali, it's a relief - freedom finally," said Cheick Sormoye, a Timbuktu resident who fled to Bamako, the capital.
Timbuktu, a city of mud-walled buildings and 50,000 people, was for centuries a seat of Islamic learning and a major trading center along the North African caravan routes that carried slaves, gold and salt. In Europe, legend had it that it was a city of gold. Today, its name is synonymous to many with the ends of the earth.
It has been home to about 20,000 irreplaceable manuscripts, some dating to the 12th century. It was not immediately known how many were destroyed in the blaze that was set in recent days in an act of vengeance by the Islamists before they withdrew.
Michael Covitt, chairman of the Malian Manuscript Foundation, called the arson a "desecration to humanity."
"These manuscripts are irreplaceable. They have the wisdom of the ages, and it's the most important find since the Dead Sea Scrolls," he said.
The militants seized Timbuktu in April and began imposing a strict Islamic version of Shariah, or religious law, across northern Mali, carrying out amputations and public executions. Women could be whipped for going out in public without wearing veils, while men could be lashed for having cigarettes.
Just over two weeks after the French began their military intervention in Mali, French and Malian forces arrived in Timbuktu overnight, the French military spokesman said Monday.
"The helicopters have been decisive," Burkhard said, describing how they aided the ground forces who came from the south as French paratroops landed north of the city.
During their rule in Timbuktu, the militants systematically destroyed cultural sites, including the ancient tombs of Sufi saints, which they denounced as contrary to Islam because they encouraged Muslims to venerate saints instead of God.
The mayor said the Islamists burned his office as well as the Ahmed Baba institute, a library rich in historical documents.