Attacks on public targets have largely diminished since the Taliban seized power in August last year, but the militant Islamic State group continues to operate across the country.
“We had finished the prayers and were heading out of the mosque when the blast occurred,” worshipper Mohammed Yasin said.
Kabul police spokesman Khalid Zadran said a grenade was thrown inside the Pul-e-Khisti mosque and a suspect was arrested at the scene.
No group has claimed responsibility, but the Islamic State-Khorasan (IS-K) group has carried out recent attacks in Kabul and other cities.
The blast was the second in a week in the Afghan capital, after another tore through the main money exchange centre, killing one person and injuring dozens.
Wednesday’s explosion occurred after someone threw a grenade at the mosque, and one person had been arrested, according to a spokesman for Kabul’s military commander.
The attacks have hit the capital after a relative lull in violence over the cold winter months.
Taliban officials insist their forces have defeated IS, but analysts say the jihadist group is a key security challenge to the hardline Islamists who now rule Afghanistan.