The court's finding has created the worst diplomatic crisis between Iran and the West since 1989, when revolutionary leader Ayatollah Ruhollah Khomeini urged Muslims around the world to find and kill British author Salman Rushdie.
Some of the roughly 400 students threw stones at the embassy in downtown Tehran, which since this weekend has been protected by a second, hastily erected 10-foot fence.
Almost 1,000 riotpolice stood six deep outside the compound and linked arms - at one point, drawing their shotguns to make it clear to the students that the would not be allowed through.
Police roughed up several students and briefly detained dozens.
It was the first violence since a Berlin court convicted four men Thursday in the 1992 murders of four Iranian dissidents in Berlin and said that the order to kill came from Iran's top leaders. Prosecutors earlier implicated Iran's supreme leader, Ayatollah Ali Khamenei, and President Hashemi Rafsanjani.
Unlike a demonstration a day earlier that drew 100,000 people, yesterday protest seemed to take the Iranian government by surprise.
"Yesterday's protest did not express the Iranian nation's anger, and today we will make it clear," Amir Fateh, a student leader, said before maching fom Tehran University to the embassy.
Fateh, who was arrested Mondaybut released an hour later, said the protesters wanted to get through the embassy gate and holda protest inside the compound "to express our anger."
In 1979, militant students seized the U.S. Embassy in Tehran and held 52 Americans for 444 days. The anniversary of the Nov. 4 takeover has become a traditional day of protest ever since.