The clashes occurred during demonstrations staged for the third night in a row to protest the against Iran’s Islamic clerical rule.
The member of an Islamic student association said that 200 members of the special forces stormed in the campus at 1:00 am (2030 GMT).
They were armed with batons and wearing helmets and engaged in clashes that lasted until 8:00 am, according to the student.
In addition to those injured, 100 students suffered from exposure to teargas fired by the police.
Protesters called on the country’s supreme leader Ayatollah Ali Khamenei to resign.
They chanted slogans like “Death to the dictator”, “Death to Khamenei” and “Khamenei, step down from the throne”.
The protesters also vented their anger on President Mohammed Khatami, who has won the elections twice mainly by the votes of the youths.
They accused him of failing to fulfill his reform promises after six years in government.
Influential former President Akbar Hashemi Rafsanjani said students could express themselves but warned them not to fall into a US trap.
“Some anti-revolutionaries, who are just wimps, chanted some slogans and now look how much America is pinning its hope on them”, he said.
But then he made a more pacifying tone, saying it was acceptable for young people to be angry and that “we shouldn’t be very sensitive about that”.
Rafsanjani heads the powerful Expediency Council that arbitrates on legislative disputes.
His comments came during Friday’s prayers after the United States said it backed the protests.
“The United States fully supports their aspirations to live in freedom”, State Department spokesman Richard Boucher said referring to the protesting students.
“It’s our hope that the voice of the Iranian people and their call to democracy and the rule of law will be heard and transform Iran into a force of stability in the region”, he said.
The protests, which began on Tuesday night, are believed to have been in response to calls made by US-based Iranian opposition satellite television channels to gather at the university and dormitories.
On Thursday, Khamenei accused the United states of trying to turn disgruntled Iranians into mercenaries.
The protests followed recent talk in US administration circles of adopting a more aggressive strategy towards Iran.
US administration officials have said that the Pentagon is pushing for a policy that aims at subverting the established Islamic system in Iran.
The United States accuses Iran of developing nuclear weapons, interfering in Iraq and sheltering members of al-Qaeda. Tehran has denied all the accusations.
After midnight, about 100 students were able to get out of their university campus by breaking down a door.
Protesters threw stones at police and members of pro-government militias.
Several hundred other students lit fires inside the campus, drawing teargas from police.
Thousands of student supporters drove their cars and honked their horns near the campus but could not get too close as the roads were blocked by anti-riot squads.
Unlike previous nights, no large crowds could be seen walking on foot in the area apparently due to the heavy security presence.
Police also did not allow members of Ansar Hizb Allah, a conservative group, from getting near the campus.
Members of the group, who rode on scooters, were armed with clubs, iron chains and walkie-talkies, witnesses said.