Ahmed Ounaies resigned after only a few weeks in office, Radio France Internationale reported.
On an official visit to France, Ounaies hailed French Foreign Minister Michele Alliot-Marie as "above all a friend of Tunisia."
Alliot-Marie is facing calls for her resignation in Paris after admitting flying on vacation to Tunisia on a jet owned by a Tunisian businessman with ties to Ben Ali. She earlier offered to help the Ben Ali regime deal with protests.
Days after his return from France, his Foreign Ministry staff protested against Ounaies. They demanded he resign immediately and he took his personal belongings and left.
A 75-year-old retired diplomat, he was named to a government of national unity on Jan. 17.