Four students were slightly injured and seven arrested in the clashes on Friday.
About 500 students gathered to mark the 15th anniversary of Aoun's declaration of a "war of liberation" against Syria. He was at the time head of a Lebanese military government.
Aoun, who has lived in France for the past decade, opposes the presence of Syrian troops in Lebanon.
On Wednesday, several Christian opposition students and soldiers were injured during clashes as police and troops attempted to prevent a demonstration from spilling outside a university campus, witnesses said.
A joint force of riot police and soldiers cordoned off the entrance to the Jesuit Universite Saint-Joseph where about 200 students from various Christian opposition groups were demonstrating, police said.
"The policy of the regime, the corruption and the dependence on Syria are at the base of the emigration of youth," said student leader Sami Gimayil, representing the "Kataeb Base," a splinter group of the Falangist party.
Lebanon has banned street protests or gatherings until after municipal elections scheduled for May.