The move marked the latest inroad by the two-week-old French mission to oust radical Islamists from the northern half of Mali, which they seized more than nine months ago.
Col. Thierry Burkhard said Monday that the town's airport was taken without firing a shot.
"There was an operation on Timbuktu last night that allowed us to control access to the town," he said Monday. "It's up to Malian forces to retake the town."
The Timbuktu operation comes a day after the French announced they had seized the airport and a key bridge in a city east of Timbuktu, Gao, one of the other northern provincial capitals that had been under the grip of radical Islamists.
The French and Malian forces so far have met little resistance from the Islamists, who seized northern Mali in the wake of a military coup in the distant capital of Bamako, in southern Mali.
Timbuktu, which has entranced travellers for centuries with its inaccessible mystique, is some 1,000 kilometres (620 miles) northeast of Bamako. During their rule, the militants have systematically destroyed UNESCO World Heritage sites in the ancient town.
A spokesman for the al-Qaida-linked militants has said that the ancient tombs of Sufi saints were destroyed because they contravened Islam, encouraging Muslims to venerate saints instead of God.
Among the tombs they destroyed is that of Sidi Mahmoudou, a saint who died in 955, according to the UNESCO website.
Timbuktu, long a hub of Islamic learning, is also home to some 20,000 manuscripts, some dating back as far as the 12th century. Owners have succeeded in taking some of the manuscripts outside of Timbuktu, while others have been carefully hidden away from the Islamists.
Hinnant reported from Paris.
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