The two gunmen fled after carrying out the attack in the I-8 locality of the city, police said.
One person died on the spot while one of the injured succumbed to his wounds, taking the death toll to two, Geo TV reported.
Emergency services shifted the injured to PIMS hospital and police have started an investigation into the incident, it said.
Allama Raja Nasir Abbas Jafri, leader of Majlis Wahdatul Muslimeen, expressed sorrow over the incident, saying the Islamabad administration has failed to prevent the crime in the capital.
A spokesman for Tehreek-e-Nifaz-e-Fiqh- Jafaria (TNFJ) also denounced the incident, saying there is no sectarian divide in the country.
No group has claimed responsibility for the attack but banned extremist group Lashker-e-Jhangvi has claimed such attacks on minority Shias and their mosques in the past.
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