A group of youths started shouting pro-freedom slogans at Nowhatta after Friday prayers ended at the historic Jamia Masjid.
Security forces deployed to maintain law and order used batons and lobbed tear smoke shells to disperse them, leading to clashes between the two sides, a police official said.
He said the protesters threw stones at security forces.
Also, violence erupted in Sopore town in Baramulla district and Sherbagh area in Anantnag district, the official said.
No casualties were reported in any of these incidents.