The Mirage 2000D crashed half way between Gao in the restive north of Mali and the Niger capital Niamey, where France has a military base.
"The crew was forced to eject following a technical failure," said French military spokesperson Gilles Jaron. "The pilot and navigator were retrieved safe and sound."
The plane, worth several millions euros, is one of six fighter jets being used by the French army in the region.
Defence Minister Jeran-Yves Le Drian last month announced that France will deploy 3,000 troops in the region to fight Islamist and other armed groups.