The clashes broke out soon after the congregational prayers ended at the Jamia Masjid and other nearby mosques and shrines, a police official said.
He said two persons suffered pellet injuries during the clashes and they have been admitted to a hospital here for treatment.
The condition of both injured is stated to be stable.
The official said intermittent clashes were going on in the area.
Earlier, moderate Hurriyat Conference chairman Mirwaiz Umar Farooq led a protest march inside the mosque precincts against Army chief's commendation card to Major Leetul Gogoi, who had tied a Kashmiri man to his jeep as a human shield against stone-pelting on April 9.
Separatists had called for peaceful protests today after the Friday prayers against the honouring of the Army officer.