After a closed-door military ceremony a day earlier, Deby addressed Chadian forces and diplomats at an event in the capital N'Djamena.
The handover of the Kossei base, the French army's last such facility in the central African country, follows Chad's surprise breaking off of military cooperation with its former colonial ruler in late November.
"We are not breaking off our relationship with France but we are ending the military dimension of this cooperation," Deby said at the base where only the Chadian flag was now flying.
Chad must build an "even stronger, better equipped army" and "forge new alliances based on mutual respect and without losing sight of the demands of independence and sovereignty", he added.
Soldiers and fighter aircraft from France have been stationed in Chad almost continuously since the country's independence in 1960, helping to train the Chadian military.
The largely desert country had been a key link in France's military presence in Africa and its last foothold in the wider Sahel region after the forced withdrawal of French troops from Mali, Burkina Faso and Niger in the wake of military coups.
France is now reconfiguring its military presence in Africa.
Senegal is negotiating the withdrawal of French forces by the end of this year and Paris's military presence in the Ivory Coast and Gabon is being cut back.
A French base in Djibouti, which hosts 1,500 troops, is being developed as a launching pad for future missions in Africa.
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