The closure of shops and businesses was ordered by a leading Muslim organisation and several separatist groups to protest the "blasphemous" caricatures in the French satirical magazine Charlie Hebdo whose offices were attacked by gunmen on January 7.
Most businesses remained closed and the roads were virtually empty in Srinagar and other towns in the Muslim-majority Kashmir valley, according to reports.
Authorities imposed restrictions on the movement of people in some areas of Srinagar's congested old town to prevent protests after Friday prayers.
The clashes broke out when police fired smoke cannisters and shot into the air to disperse a group of protestors who began chanting slogans in favour of Islam and ‘Down with Charlie Hebdo’ after emerging from mosques.
There were no immediate reports of injuries.
Similar protests have been seen in many other parts of the Muslim world since Charlie Hebdo printed the cartoons in a defiant response to the massacre at its Paris offices in which 12 people were killed.
Security forces are on a heightened alert across India as the country prepares to welcome US President Barack Obama for its Republic Day celebrations on Monday.
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Somebody creates cartoon and peoples start killing and destroying public property.