A day after President Bashar al-Assad scrapped emergency rule, his forces opened fire with live rounds to disperse the crowd in the central protest hub, wounding at least two people, the activist said on condition of anonymity.
Thousands of protesters also swarmed the streets of the northeastern city of Qamishli, southern flashpoint town of Daraa and Midan in Damascus, where an activist reported they were also dispersed by security forces, without elaborating.
"Freedom, freedom," and "God, Syria, freedom, that's all," the protesters, who witnesses said numbered around 6,000, chanted in Qamishli as they carried a giant Syrian flag.
Several thousand called for the fall of Assad's regime in Daraa, a key focus of the unprecedented demonstrations that broke out more than a month ago.
Assad, in power since replacing his father Hafez as president in 2000, issued decrees yesterday to overturn the state of emergency as well as abolish the state security court and allow citizens to hold peaceful demonstrations.
The demonstrations came after call by Facebook group The Syrian Revolution 2011 for rallies spanning the Christian and Muslim faiths on "Good Friday," which commemorates Jesus Christ's crucifixion.
Friday is also the Muslim day of rest when the biggest demonstrations have been staged across Syria after weekly prayers in mosques.
In Qamishli, a majority Kurdish city with Muslim and Christian communities, the protesters who started their march outside Qasmo mosque chanted "Liberty, fraternity," said one witness.
"Arabs, Syriac (Orthodox) and Kurds against corruption," said a banner they brandished.
In Daraa, a Syrian human rights activist said thousands of demonstrators staged a protest calling for the fall of Assad's regime and demanding the dissolution of his feared security services.
"Around seven to 10,000 people emerged from mosques and marched to the Saraya Square (governor's HQ) in Daraa," said a witness contacted by AFP by telephone from Nicosia.
The protesters called for "the abrogation of Article 8 of the constitution which describes the ruling Baath Party as the leader in the state and in society," the witness said.
Demonstrators also called for "the dissolution of the security services as well as the fall of the regime," the witness added.