It was held after Friday prayers with the participation of the worshippers.
Roknabadi went missing after the deadly crush of pilgrims in Mina, Saudi Arabia, on September 24.
Thousands of pilgrims, including over 460 Iranians, were killed in the tragic incident.
Roknabadi’s body was only identified on Wednesday, two months after the Mina tragedy.
His body that arrived in Tehran earlier on Friday will be laid to rest at a holy site north of Tehran.
Referring in his Friday prayers sermons to the identification of the body after a long time, Ayatollah Movahedi Kermani, Tehran’s interim Friday prayers leader, said the Muslim world should be thinking of proper management of Hajj.
Saudi authorities have come under fire for their inability to ensure the safety of hundreds of thousands of pilgrims who converge on Mecca every year.
Earlier on September 11, a massive construction crane crashed into Mecca’s Grand Mosque in stormy weather, killing at least 107 people, including 11 Iranians, and injuring 201 others.