Many chanted anti-US slogans as they sat under a tower in Sadr City where an Iraqi was killed on Wednesday when US troops fired into a crowd of protestors.
In his sermon, Shaikh Abdul Hadi al-Taraji denounced the occupation forces that ousted Saddam Hussein, saying they were interested only in Iraq's "strategic wealth".
But he warned his followers not to take any action unless instructed to do so by the Hawza, Iraq's foremost Shia religious authority.
Many residents of Sadr City saw Wednesday's killing as an attack on their religion.
"We will fight against the enemies of the Prophet (Muhammad)," some chanted.
The top US soldier in Iraq, Lieutenant General Ricardo Sanchez, said his army had apologised to Shia imams over the clash.
The incident was sparked when American troops in a helicopter removed a religious flag from the communications tower in the predominantly Shia suburb.
The US army has apologised for
an attack on Shia protestors
But Sanchez said the helicopter had inadvertently blown down the flag and soldiers had not removed it intentionally.
Sanchez also said the Iraqi killed was a man who fired a rocket-propelled grenade at US troops.
However, residents said the victim was a young boy.
Shaikh Taraji is close to Moqtada Sadr, one of the most outspoken voices of Shia protest against the US occupation of Iraq.
He is arguably the most influential voice in Sadr City, but has no such authority in the wider Shia community in Iraq.
The neighbourhood of two million people, previously called Saddam City, has been renamed after grand Ayat Allahs Muhammad Baqer al-Sadr and Muhammad Sadeq al-Sadr.
Both were killed by Hussein's former regime.
Shias are a minority in the larger Muslim world but make up 60% of Iraq's 25-million population.