Police said clashes broke out on Saturday after Shia youth tried to force shopkeepers in the central district of sprawling city to close down their businesses.
"One person was killed and two others were wounded," a police official said on the condition of anonymity. He said he had no other details.
Fayyaz Qureshi, a senior police official, said more than two dozen protesters were detained for throwing stones at vehicles and shops.
Earlier, police used batons and tear gas to disperse angry mourners outside the main Shia mosque in the volatile port city.
"Stop killing innocent Shia!" shouted a crowd of about 200 mourners during a funeral procession for one of the victims killed when a powerful bomb was detonated during Friday prayers in a mosque in Karachi's business district.
Some of the protesters suffered minor injuries in scuffles with police, who struggled to control the crowds.
Grieving relatives of at least a dozen victims buried their dead as authorities deployed paramilitary troops at Shia religious sites in the volatile port city of 14 million people.
Additional police were deployed in the city amid fears of further violence.
Pakistan has seen a wave of sectarian attacks in the last year in which more than 125 people have been killed, most of them Shia.
Business centres in Shia areas were closed after community leaders called three days of mourning.
No group has claimed responsibility for the attack, but it bore the hallmarks of a sectarian attack carried out by a small group of Sunni extremists.
Angry youths that torched two
mini buses were arrested
Fayyaz Leghari, the city's police chief of investigations, said police suspected one of two mutilated bodies found could be that of the bomber.
They later released a sketch of the suspect and announced a 2.5 million rupee ($43,410) reward for information about the bomber. The motive for the attack was still unknown.
"We are working on three or four leads at the same time, including the involvement of militant groups," he said.
Plastic bombs used
However, he said it was premature to say whether the most violent Sunni sectarian group, Lashkar-i-Jhangvi, was behind the attack.
Ajmal Magsi, chief of city's bomb disposal department, said the bomber may have used plastic explosives.
"The bomb weighed over two kg and the suicide bomber was hiding explosives beneath his clothes".
Pakistan has suffered decades of violence between the minority Shia and small groups in the Sunni majority.
In March, 44 people were killed and 150 wounded in an attack on a Shia religious procession in the southwestern city of Quetta that was blamed on Sunni extremists.
Pakistan’s Shia, who account for about 15% of the population, largely live at peace with Sunnis. Most of the violence is perpetrated by extremist groups from both sides.