It was the first time police and protesters had clashed inside university premises since the Conservative government's abolition of academic sanctuary earlier this year.
With about 200 students rallying outside the University of Economics and Business, several dozen broke through the locked gate and entered the front yard, witnesses said, Presstv Reported.
Police fired gas and firecrackers to disperse them, as some students threw stones and scuffled with officers while others clapped and chanted slogans.
On Sunday, police had entered the university to grab motorbike helmets, face masks, fire extinguishers and other materials they said were used in attacks and protests.
University authorities decided to shut it for a week.
Leftist parties say the concept of academic sanctuary, which prohibited security forces from entering universities, protected students' freedom of expression. But the government, which came to power in July, said it had been a cover for lawlessness.
The sanctuary law was a legacy of a crackdown by the then military junta on students on November 17, 1973, when a tank burst through the gates of the Athens Polytechnic, killing dozens, and leaving deep-rooted suspicion towards authority among Greeks.
Monday's violence came a week before an annual march to mark that 1973 student revolt. The march often becomes a focal point for anti-government protests and clashes in the bohemian Exarchia discrict, which is surrounded by universities.