Mohamed Hammami was subject to "expulsion from French territory. He has been deported to Tunisia, where he is a citizen," the ministry said in a statement.
"In his sermons," Hammami "encouraged violent jihad, made anti-Semitic remarks and justified the use of violence and corporal punishment against women," added the ministry.
"These unacceptable, deliberate, repeated provocations and discrimination constitute a threat to French society and security."
The imam's son Hamadi Hammami told AFP he believed France's DCRI domestic intelligence service had arrested his 77-year-old father in the streets before taking him to the airport.
In January, former interior minister Claude Guéant accused Hammami, who had been living in France for a long time, of making violent anti-Semitic remarks and of calling for adulterous women to be flogged to death.
Hammami, whose assets were frozen by the government in May, has denied all the allegations.
A deportation committee had issued in May a statement against expelling Hammami because it would "affect his family life", but the opinion only carried advisory weight.