Some 3,000 demonstrators gathered in Imam Hossein Square in eastern Tehran, chanting slogans against Saudi Arabia's Al-Saud royal family following the kingdom's execution on Saturday of Sheikh Nimr al-Nimr.
His death has sparked fury among Shiites across the Middle East with protests erupting in several countries.
A mob on Saturday firebombed the Saudi embassy in the Iranian capital and a consulate in second city Meshhad, triggering regional and international condemnation.
The assaults prompted Riyadh to break off diplomatic ties with Iran and order its diplomats to leave the kingdom. Saudi allies Bahrain and Sudan have followed suit and the United Arab Emirates downgraded its ties with Iran.
Others torched the flags of Israel, Iran's arch-foe, and of the United States which is one of Saudi Arabia's key Western allies.
The Saudi flag which bears the Islamic statement of faith -- words that are holy to all Muslims -- was not set of fire.
Hundreds of merchants from Tehran's Grand Bazaar also shuttered their shops and took part in the anti-Saudi protests.
