At least 40 police officers and four students were injured during the clashes outside Tehran University's dormitories on Tuesday night and Wednesday morning.
Six students were arrested during the protest.
Abdollah Momeni, a student leader, said up to 2,000 students had gathered for the protest over the expulsion of some students and the authorities' handling of critics.
He added that 20 had been seized by Islamic vigilantes who broke into the dormitories.
"The main reason for the objections in recent days goes back to the limitations imposed on universities and political students after the new government came to power," Momeni said.
Ahmadinejad, a religious conservative, was elected president in June.
"Some active students have been expelled and some students face mass summons before disciplinary committees. We are also objecting to recent dealings with critical professors such as Ramin Jahanbegloo," he added.
Iran this month said it had arrested philosopher Jahanbegloo – a liberal who favours strengthening ties with the West - on charges of espionage.
Meanwhile students at Tehran's Amir Kabir university also launched protests against the alleged intervention of the Basij - an Islamic militia - in student elections.
"We don't want the Islam of the Taliban" shouted students, according to the ISNA news agency