Iran is staging mass funeral processions for Khamenei - whose 37-year reign was brought to an end in February by the first airstrike of the war launched by the US and Israel - in a show of public devotion to the Islamic Republic's theocratic state and revolutionary zeal.
Television footage showed his coffin draped with the Iranian flag and topped with his black turban.
It was placed, along with four other coffins of his slain family members, on a large black platform that resembled the Kaaba, the cube-shaped structure at the centre of Islam's holiest site in Mecca.
The vast courtyard of the complex, the Imam Khomeini Grand Mosalla, was filled with mourners, many waving Iranian flags and carrying photographs of the slain leader.
"'Death to America' chants echoed through Tehran's Mosalla on the day of the farewell to 'Mr Martyr'," state broadcaster Seda va Sima said.
In video posts on other state media news sites, mourners were also heard chanting: "Our slogan is one word: Revenge, revenge," and "We will kill, we will kill he who killed our Imam."
Water misted from rooftops to cool mourners in the summer heat. Khamenei's coffin will remain in the Mosalla until Sunday evening.
His body was expected to be taken to Qom, Najaf and Kerbala, the great Shi'ite centres of Iran and Iraq, before being laid to rest on Thursday in Mashhad, home to the country's holiest pilgrim shrine.
The coffin was unveiled late on Thursday to a throng of sobbing supporters, who were swaying and beating their heads in time to a sung lament as flowers were thrown into the crowd.
On Friday the coffin was laid in state in the great prayer hall built to honour his predecessor, Ayatollah Ruhollah Khomeini.
Authorities plan to mobilise millions of people for big processions over the coming days, offering transport, food and lodging to buoy the numbers.
The new supreme leader, Khamenei's son Mojtaba Khamenei, has not been seen in any new image since being wounded in the strike that killed his father.
