Police had to fire dozens of tear smoke shells in an attempt to disperse the stone-pelting students from S P College and the adjoining Women's College on M A Road, officials said.
They said the clashes emanated from S P College and soon spread to the streets of Regal Chowk and adjoining areas.
The students from the Women's College also joined the protests, which spread to other parts of the commercial hub, the officials said.
The clashes led to closure of the markets and the people rushed to safer locations out of the commercial hub, the officials said.
The violence was witnessed on a day the colleges reopened in the valley after a gap of five days.
The authorities had shut the higher educational institutions as a precautionary measure in the wake of widespread violence by the students in Kashmir on Monday against the alleged high handedness of security forces with students in Pulwama on April 15.