Without a shot being fired to stop them, 1000 French soldiers – including paratroopers – and 200 Malian troops yesterday seized the airport and surrounded the centuries-old Niger River city, looking to block the escape of al Qaeda-allied fighters.
The retaking of Timbuktu followed the swift capture by French and Malian forces at the weekend of Gao, another major northern Malian town which had also been occupied by the alliance of Islamist militant groups since last year.
A two-week intervention by France in its former Sahel colony, at the request of Mali's government but also with wide international backing, has driven the Islamist rebel fighters northwards out of towns into the desert and mountains.
A French military spokesman said the assault forces at Timbuktu were being careful to avoid combat inside the city so as not to damage cultural treasures and mosques and religious shrines in what is considered a seat of Islamic learning.
However, Timbuktu's mayor, Ousmane Halle, reported fleeing Islamist fighters had torched a South African-funded library in the city containing thousands of priceless manuscripts.
Speaking from the Malian capital Bamako yesterday, Mr Halle said: "The rebels set fire to the new Ahmed Baba Institute. This happened four days ago."
He claimed he had received the information from his chief of communications who had been in Timbuktu. Mr Halle was not able to immediately say how much of the concrete building had been damaged. He added the rebels also torched his office and the home of a member of parliament.
The Ahmed Baba Institute, one of several libraries and collections in the city, contains fragile ancient documents dating back to the 13th century.
The United States and European Union are backing the French-led Mali operation as a strike against the threat of radical Islamist jihadists using the West African state's Sahara desert as a launch pad for international attacks. They are helping with intelligence, airlift of troops, re-fuelling of planes and logistics, but do not plan to send combat troops to Mali.
"Little by little, Mali is being liberated," said French Foreign Minister Laurent Fabius.
At Gao, more than 190 miles east of Timbuktu, jubilant residents danced to music in the streets on Sunday to celebrate the liberation of this other ancient Niger River town from the sharia-observing rebels.
A third northern town, the Tuareg seat of Kidal, in Mali's rugged and remote north-east, remains in the hands of the Islamist fighters, a loose alliance that groups AQIM with Malian Islamist group Ansar Dine and AQIM splinter MUJWA.
As the French and Malian troops push into northern Mali, African troops from a United Nations-backed continental intervention force – expected to number 7700 – are being flown into the country, despite severe delays due to logistical problems.
The outgoing African Union chairman, President Thomas Boni Yayi of Benin, also urged other Nato members and Asian countries to follow France's lead and send troops to Mali.
"We have to free the Sahel from the threat of terrorism," he said.