Hundreds of Palestinians also rallied in the West Bank city of Ramallah to show support for Americans killed in the attacks, as well as condemn Israeli killing of Palestinians in Jenin.
And in Iran, Tehran's main football stadium observed an unprecedented minute's silence in sympathy with the victims.
'State terrorism'
Iran's Ayatollah Imami Kashani spoke of a catastrophic act of terrorism which could only be condemned by all Muslims, adding the whole world should mobilise against terrorism.
But if its roots were really to be tackled, terrorism and its practitioners would have to be defined, he said, pointing to Israel and calling it a "terrorist state which was killing children".
America's support and its arrogant policies around the world might help to explain the brutalism of the hijackers, he added.
On Thursday night, people who tried to stage a commemorative vigil in central Tehran, in spite of the ban on public gatherings, were broken up by police and Islamic volunteers.
'Barbaric acts'
The head of al-Azhar in Cairo, one of Sunni Islam's highest religious authority, said attacking innocent people was not courageous, but stupid and would be punished on Judgement Day.
"It's not courage in any way to kill an innocent person, or to kill thousands of people, including men and women and children," said Sheik Mohammed Sayed Tantawi.
In Lebanon the spiritual leader of the Shia guerrilla group, Hezbollah, called the attacks "barbaric acts".
He added even though Muslims were opposed to the American Government because of its support for Israel, the American people should not be blamed.
No mention
One imam in the Nuseirat refugee camp outside Gaza City said Islam should not be tarred by association, even if chief suspect Osama Bin Laden was eventually tied to the attack.
The imam pointed to the lessons of the 1995 Oklahoma City bombing, in which he said "Christianity, America, or the Christian world were not accused because a Christian masterminded it."
In Iraq, a nationally televised sermon from Baghdad's al-Azam mosque urged that no tears be shed for "tyrants whose hands are stained with the blood of our people".
And at the al-Ansar mosque in the West Bank town of Hebron, where supporters of the militant Islamic movement Hamas were heavily represented among worshippers, the sermon did not mention the US attacks.