Iran does not have diplomatic ties with the United States and U.S. interests in Tehran are handled by the Swiss embassy.
About 1,000 protesters, chanting "Death to America" and "U.S. pastor must be killed," threw stones at the building of the embassy.
Although pastor Terry Jones dropped his plan to burn copies of the Islamic holy book on the anniversary of the September 11 attacks on the United States, the plan sparked outrage around the world and triggered violent protests in Afghanistan and Indian Kashmir.
Iran's Supreme Leader Ayatollah Ali Khamenei on Monday called the plan to burn the Quran "an insane and hateful" act and blamed "the Zionists working within the American government" for masterminding it.
"With deceiving and half-empty words, the leaders of the American regime cannot acquit themselves of ... accompanying this ugly act," Imam Khamenei was quoted as saying by state television.
"To prove its claim of not being involved ... the American government should appropriately punish the main figures behind this great crime," he added.
At Monday's protests, some demonstrators were holding copies of the Quran and others wore white funeral shrouds showing they were ready for martyrdom against insult to the holly Quran.
Iran's state television showed pictures of other demonstrations throughout the country on Monday.
"Stopping the Quran burning plan ... is not enough and the American government should be responsible and take pre-emptive measures," Foreign Ministry spokesman Ramin Mehmanparast was quoted as saying on Monday.
Grand Ayatollah Lotfollah Safi said Muslims would not be "satisfied with only condemnations" of the plan and that the world expected to see an appropriate response by U.S. leaders, Isna news agency reported.
U.S. President Barack Obama appealed to Americans last week to respect the "inalienable" right of religious freedom and expressed hope Jones would abandon his plan.
Imam Khamenei made clear the "incident had nothing to do with Church and Christianity."
"We Muslims will never act this same way with the sanctities of other religions," he said.
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