Several hundred young Iranians had gathered outside the embassy on Wednesday as about 100,000 people gathered in the vast Enghelab (Revolution) square.
Iranian authorities called for the demonstration in response to the profanation of Shia holy sites in Iraq, blamed on US-led occupying forces.
They also burned US and British flags and hurled them at the embassy, but were prevented by police from crossing the road to get nearer to the mission.
Some demonstrators and a number of photographers were arrested.
Earlier tens of thousands marched through Tehran towards the central square, three kilometres from the embassy, burning US, British and Israeli flags and screamed "Death to America, Death to Israel".
Government sponsored demo
The clerical Iranian government had called for the demonstrations in Tehran and the holy cities of Qum, south of the capital, and Mashhad in the northeast.
"Muslims cannot tolerate the insolent attacks by US soldiers against the holy places, and these crimes can only be condemned in the eyes of the Islamic world, the Shia and the Iranian people"
Ayat Allah Ali Khamenei
For several days the authorities have denounced actions by US forces against the militia of Iraqi Shia leader Moqtada al-Sadr, in particular in the cities of Najaf and Karbala.
But they have refrained from voicing support for al-Sadr in his rebellion against the US-led "coalition" occupying Iraq.
Officially Tehran supports Grand Ayat Allah Ali al-Sistani, the most respected of Shia religious leaders in Iran, who has called on both sides to leave the Shia holy cities.
Iran's supreme leader, Ayat Allah Ali Khamenei, said on Sunday "Muslims cannot tolerate the insolent attacks by US soldiers against the holy places, and these crimes can only be condemned in the eyes of the Islamic world, the Shia and the Iranian people."
He also said the prisoner abuse scandal at the US-run Abu Ghraib jail outside Baghdad represented "a shameful stain which cannot be easily wiped clean" by the US.
Iranian protesters called for a US
withdrawal of Iraq
On Sunday, several hundred Islamic students threw rocks at the British embassy in Tehran and tried to storm the building in a protest over the US-led occupation, but were turned back by riot police.
The United States has had no diplomatic relations with Iran since shortly after the Islamic revolution of 1979 which ousted the Shah
Iran's influential former president Akbar Hashemi Rafsanjani said the "worst mistake of the United States was to have caused trouble in the Shia regions of Iraq."
"The world's 200 million Shia Muslims will never forget the crimes of the Americans," he warned.
Also on Sunday the Iranian military said in a statement that "The US occupiers should know that they are responsible for any desecration of holy sites in Iraq and they had better heed warnings and advice of the supreme leader ... and stop their crimes."
Iran's population is 90% Shia Muslim.