The riots broke out in the southern port city on Saturday after two gunman on a motorcycle killed Abne Hasan, a doctor.
Police said the shooting, which occured in the eastern party of the city before noon, appeared to be a sectarian attack.
"It was a targeted killing. He was shot dead in front of his house," said Tariq Jameel, the city's deputy police chief.
Dozens of people - mostly angry Shia Muslim youngsters - suffered minor injuries in scuffles with police, who struggled to control the crowd.
Another police official said protestors torched two cars, one motorcycle and a state-run bank, and blocked the city's main Sharah-e-Faisal road.
No group claimed responsibility for the killing, which came just over a month after at least 53 people were killed in a sectarian attack on a Shia mosque in the southwestern Pakistani city of Quetta, close to the Afghan border.
A mainly Sunni Muslim country, Pakistan has been wracked by sectarian attacks which have been stepped up this year.