Local newspaper Midi Libre reported that around four young men burst into the Saint Joseph church on Saturday evening and started throwing the stones.
There were around 150 people in the church at the time.
The newspaper said the youths were of "north African descent."
Some of the parishioners tried to catch the youths before they fled.
Nobody was injured in the attack although many of the churchgoers were reported to be "deeply shocked."
The Saint Joseph church is in a sensitive neighbourhood of the city with the neighbouring La Conte housing estate close by.