The blast, in the southern city of Karachi, killed a worshipper and injured more than a dozen people on Monday. It was preceded by a shootout that left another attacker, a police officer and a guard dead.
A crowd outraged by the attack went on a rampage afterwards, torching cars and shops nearby. Eight people were injured in the violence.
The attack occurred during evening prayers at the Madinat al-Ilm Imambargah in eastern Karachi, said Asif Ijaz, a police official.
The three attackers stole an automatic weapon from a police guard who was posted outside the mosque and shot him dead, Ijaz said.
Other policemen nearby opened fire, killing one of the attackers and injuring another. The guard was also killed in the shootout.
The third attacker managed to enter the mosque and detonate a bomb strapped to his body.
One worshipper died and four were seriously injured in the blast. Sixteen others were treated at local hospitals, said Zafar Hussain, an administrator of the mosque.
Police, however, said the blast was weak. "It appeared to be a low-intensity bomb because it did not cause major damage," said Mushtaq Shah, chief of police operations in Karachi.
Sectarian attacks are common
About 1000 outraged mebers of the Shia community, many beating their chests in mourning, burned about a dozen vehicles, a restaurant, two gas stations and eight shops near the mosque, Ijaz said.
Two electricity transformers were also set on fire, plunging the mosque and the neighbourhood into darkness as mobs burned tires.
The bomber was believed to be a man in his 20s.
Rauf Siddiqi, home minister of Sindh province of which Karachi is the capital, condemned the bombing and said security has been put on "high alert".
"These incidents are happening one after the other. We are trying to find a link between them," he told the Geo television station. "This is a criminal and merciless attack."
The attack came three days after a suspected bomber attacked a Shia religious gathering during a festival at a shrine near Islamabad, Pakistan's capital, killing about 20 people and injuring dozens of others.
"These incidents are happening one after the other. We are trying to find a link between them. This is a criminal and merciless attack"
Sindh province home minister
Political and sectarian violence between groups within the majority Sunni and minority Shia Muslim communities is common in Karachi.
Earlier in the day, assailants shot dead a senior official from Pakistan's largest Islamic group after he was kidnapped from a funeral for another slain member of the party, police said.
Police found the body of Aslam Mujahid, 47, riddled with bullets near a college in Karachi's eastern Korangi neighbourhood, hours after he was kidnapped, said Tariq Jamil, a senior Karachi police official.