The students, who were marching to demand the release of protesters arrested in recent days, massed in eastern Caracas. But the demonstration quickly became violent when they targeted the Tourism Ministry and riot police intervened.
It was the latest chapter in months of turbulence in the oil-rich but economically and socially troubled South American country.
At least 42 people have died and more than 800 have been injured since students and other opponents of the socialist government of President Nicolas Maduro took to the streets in February to protest rampant crime, runaway inflation and shortages of basic goods.
Manuel Quevedo, commander of the National Guard regiment in Caracas, said 16 women and 89 men were arrested Wednesday, including 11 minors. He had earlier indicated that about 80 arrests had been made.
Local non-governmental group Foro Penal confirmed the tally.
While declining to confirm how many civilians were wounded in the clashes, Quevedo said two members of the security forces were wounded.
One captain of the National Guard was assaulted, while another sergeant almost got rolled over by vehicles due to protesters trying to prevent the transfer of detainees to prison, according to the military chief.
"Everything has been done with respect for human rights," he added.
Trucks carrying the detainees tried to move along the main route of the Caracas district of Chacao, heart of more than three months of opposition protests, amid a crowd shouting "Let them go!"
Last week, more than 200 people were arrested in police raids on encampments of protesters in Caracas. Most have since been freed.
"Fewer and fewer people are heeding protest calls. Intimidation has succeeded," one of the young marchers told AFP, requesting anonymity after a previous arrest.