City officials said the university dean suffered head injuries when youths raided the building and was rushed to hospital.
Clashes also continued overnight at Athens Polytechnic, where masked youths emerged to hurl rocks and bottles at police, who responded with tear gas.
Earlier in Thessaloniki - Greece's second-largest city - demonstrators threw petrol bombs at police and smashed the storefront of a Starbucks cafe, Associated Press reported.
To head off trouble, riot police carried out a series of raids on Saturday across Athens, arresting more than 150 people, reports said.
The BBC's Malcolm Brabant in Athens says they have been forming snatch squads to deal with breakaway groups apparently intent on causing damage.
Greece's government warned it would have a zero tolerance policy towards violence.
"We want to send a clear message, we won't tolerate a repeat of the violence and terror scene in central Athens, we won't hand Athens to vandals," said Citizen Protection Minister Mihalis Chrysohoidis.
Family and friends of teenager Alexandros Grigoropoulos held a memorial service in the Exarchia district of Athens on Sunday evening to mark a year since his killing.
At one point an anarchist group took over buildings at Athens University
They appealed for calm, but posters had appeared in the capital saying: "We won't forget, we won't forgive."
On Saturday, two cars were set alight in the Exarchia.
Police said up to 150 foreign anarchists arrived this weekend from Italy, France and other European countries.
Greek Prime Minister George Papandreou had acknowledged the weekend was a "crucial moment" for his new socialist government and for the nation.
"All of us, citizens, political leaders, parties, students representatives, we must protect Athens," he said.
Two police officers have been charged with the murder and attempted murder of Alexandros Grigoropoulos. Their trial is due to begin in the New Year.
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