The demonstration took place outside a Cairo mosque where Saudi preacher Mohammed al-Oreifi called in a sermon for a "jihad in the cause of Allah in Syria."
Oreifi urged worshippers to "unite against their enemy."
Saudi Arabia, like Egypt, is an overwhelmingly Sunni Muslim country, and Sunnis are the backbone of the revolt against Assad, whose Alawite sect is an offshoot of Shiite Islam.
Demonstrators, most of them bearded and wearing the traditional white galabiya, shouted "there is no God but Allah, and Bashar is his enemy."
Yesterday, influential Sunni clerics from several Arab states called for a holy war against the "sectarian" regime in Syria.
"We must undertake jihad to help our brothers in Syria by sending them money and arms, and providing all aid to save the Syrian people from this sectarian regime," they said in a statement at the end of a gathering in Cairo.
They called the "flagrant aggression" of Iran and the Lebanese movement Hezbollah -- both Shiite -- and their "sectarian allies" in Syria "a declaration of war against Islam and Muslims."
Sunni-dominated Saudi Arabia's top cleric Abdulaziz al-Shaikh has urged governments to punish the "repulsive sectarian group" while Qatar-based Sunni cleric Yusuf al-Qaradawi has called on Sunnis to join the rebels.
Hezbollah's intervention in Syria, which helped Assad's troops overrun the strategic town of Qusayr, has been roundly condemned by Arab countries.
In Cairo, a senior aide to President Mohamed Mursi demanded yesterday that the group "immediately end" its involvement in Syria.
The Shiite group's assistance to Assad could "further turn this conflict into a sectarian conflict that will spill over into the entire region," Khaled Al-Qazzaz said.
"The right of travel or the freedom of travel or taking certain positions is open for all Egyptians," he told reporters at a briefing.
"But we did not call on Egyptians to go and fight in Syria," he said.
Egypt believes the conflict will have to be resolved politically, he added.
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