"Damnation upon France!" the protesters chanted, waving the black flags adopted by jihadists.
The demonstration was in response to a cartoon published by French satirical magazine Charlie Hebdo of the Prophet Mohammed, a week after a January 7 attack at its Paris headquarters killed 12 people.
Some of the protesters also carried pictures of the Islamist brothers Cherif and said Kouachi who carried out the attack which was claimed by Al-Qaeda.
"Leave Gaza, you French, or we will slaughter you by cutting your throats," chanted the protesters.
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Palestinian police arrested dozens of people who tried to break into the French cultural centre, which has been closed since it was damaged in a fire last October.
Protest graffiti was sprayed outside the centre before dawn Saturday, following Wednesday's cover cartoon of Prophet Mohammed in Charlie Hebdo.
"You will go to hell, French journalists," read one of the slogans.
Depictions of the prophet are considered forbidden in Islam and the latest one has sparked angry protests across the Muslim world, some of which turned deadly.