Police said two gunmen were involved in the attack at the Babul Ilam imambargah located in I-8 Sector of the capital.
The gunmen fled after carrying out the attack, they said.
One person died on the spot while one of the injured succumbed to his wounds, Geo TV reported, citing police.
Emergency services shifted the injured to hospital and police have started an investigation into the incident.
Majlis Wahdatul Muslimeen, a Shia political organisation, leader Allama Raja Nasir Abbas Jafri expressed sorrow over the incident and said the Islamabad administration has failed to prevent the crime in the capital.
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He said they have foiled such conspiracies in the past and will continue to do so.
A spokesman for Tehreek-e-Nifaz-e-Fiqh-Jafaria, a Shia political party, also denounced the incident, saying there is no sectarian divide in the country.
No group has claimed responsibility for the attack but Sunni extremist groups linked with the Taliban such as Lashker-e-Jhangvi often carry out attacks against minority Shias.
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