Pro-Muslim Brotherhood students from Ain Shams University blocked the vital Al-Khalifa Al-Mamoun street in Heliopolis Thursday while marching from campus towards the Defense Ministry.
A number of protesters threw stones at military police around the ministry.
Security forces fired tear gas, causing a number of students to be suffocated, as well as water cannons. No deaths were reported.
Barbed wire has been installed around the perimeter of the ministry.
Dozens of female students from Al-Azhar University joined the march, raising the four-finger Rabea al-Adaweya sign and chanting slogans against the army and police.
Students ended the protest this evening and returned to campus.
In the southern city of Minya, Pro-MB students shut down the gates of the Faculty of Engineering, preventing students and professors from going in and starting a strike in protest of the arrest of 13 fellow students at a demonstration.
The 13 pro-MB students were arrested last week for rioting, and are facing the charges of injuring a police officer, causing damage to vehicles and breaking the newly-instated protest law, which requires prior authorization for demonstrations.
Egyptian universities have been witnessing a rising tide of demonstrations denouncing the current regime that ousted Morsy in July.
Edited translation from Al-Masry Al-Youm