Tariq Arian, spokesman for the Afghan Interior Ministry, said the bomb targeted the Wazir Akber Khan Mosque at around 7:25 pm, when worshipers had gathered for evening prayers.
Mullah Mohammad Ayaz Niazi was one of two people killed in the attack, Arian said. He was wounded in the attack and died later at a hospital.
Niazi was a well known cleric who was active as Friday prayer leader at the mosque.
No one immediately claimed responsibility for the attack, but the Islamic State group has been active in Kabul in recent weeks and has in the past carried out attacks inside mosques in Afghanistan.
Taliban insurgents have never carried out an attack inside of a mosque.
The IS claimed responsibility for the roadside bomb attack against a bus belonging to a local TV station in Kabul on Saturday, killing two employees of the station.
Attacks against worshippers have increased in Afghanistan: Last month, an unknown number of attackers stormed a mosque in northern Parwan province, killed 11 worshipers and wounded several others.
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