Thousands of people, including Afghans nationals, attended the funeral.
Ayatollah Kaboli was laid to rest at the holy mausoleum of Hazrat Masoumeh (SA).
On Friday, a memorial service was held for the senior cleric at the Azam Mosque in Qom.
Ayatollah Kaboli died on Tuesday morning at the age of 91.
At the age of 7, he started learning the Quran and Persian reading and then Islamic teachings and Arabic literature.
Kaboli continued his religious education in Kabul and then left for the holy city of Najaf, Iraq, to study at the prestigious seminary there.