The attack on the mosque in Carpentras occurred on Friday and caused only minor damage, the Vaucluse regional government said in a statement. No one was injured.
The attack was condemned by President Jacques Chirac and Prime Minister Dominique de Villepin, who are struggling to contain more than two weeks of rioting across the country.
It was not immediately clear if the attack was directly linked to the wider unrest.
Chirac expressed his solidarity with the town's Muslim community and assured them that "light will be shed on the circumstances surrounding this attack", his office said in a statement.
"All steps will be taken to identify the culprits and bring them to justice so that they answer for this particularly unacceptable act," De Villepin's office said in a statement early on Saturday.
An unidentified attacker threw the firebombs at the mosque's entrance hall during Friday prayers and fled, the regional government said. He was pursued by two witnesses but escaped, it added.
About 20 worshippers inside the mosque quickly put out a fire started by one of the bombs and activities inside the mosque quickly resumed, the statement said.