The bomb exploded at the entrance of Saleh mosque, located close to the Arambagh police station in Karachi, when people were coming out after prayers.
This is the first time that a bomb attack has been carried out at a mosque of the Bohra community in Karachi.
A doctor at the Civil hospital, where the injured were brought, said two people had died.
Panic and fear spread in the busy commercial area immediately after the blast.
In recent times extremist Sunni Muslim groups have carried out suicide bomb attacks on Shia Muslims.