The protesters broke away from a peaceful rally and hurled rocks and firebombs at police and buildings near parliament, overturned a car and set fire to trash bins. They also splashed police with red paint.
Police responded with tear gas and flash grenades.
Firefighters and police also rushed to stop protesters from burning down the city's main Christmas tree, which was just replaced earlier this week after the first was torched in riots. Families abandoned the carousel in downtown Syntagma Square after happily going on rides all morning.
Thursday's clashes were the latest outbreak of violence after the police's fatal shooting of 15-year-old Alexandros Grigoropoulos Dec. 6. Protests over the boy's death and the increasing economic hardship inhave led to the worst rioting the country has seen in decades.
Hundreds of businesses have been smashed, burned or looted and gangs of youths fought running battles with riot police firing tear gas every night for a week. The riots have been fed by dissatisfaction with Greece's increasingly unpopular conservative government.
More than 200 youths took part in running battles with police Thursday in Athens. They also set fire to a private security van and set up a burning barricade after smashing a cafe storefront, and dragging out and setting fire to its furniture. Downtown streets were littered with smashed paving stones and marble blocks.
Shop owners who saw their businesses smashed and looted during the initial riots last week now say they are having trouble making ends meet because many customers are staying away from the city center.
"Who's going to pay all these bills? I'm taking in euro200 ($290) a day," complained Spyros Papaspyrou, the owner of a shoe shop in central Athens. "Do they want me to stand outside my shop with a shotgun? I can't understand why they can't arrest 80 people in the center of Athens."
Before the violence broke out, some 7,000 students and other protesters marched in a rally, chanting "We are the law, we'll stay on the streets." As they passed, fearful shop owners shuttered their store fronts. Some demonstrators painted white crime-scene-style body outlines on the streets.
Earlier in the day, some 1,000 demonstrators joined a peaceful Communist Party-backed march through the city. Some 300 people also marched in Greece's second largest city of Thessaloniki.
While sporadic rallies have been held in Europe in support of the Greek protesters, none were reported Thursday.
Major labor union staged work stoppages Thursday to protest the teenager's shooting and the conservative government's economic policies.
Air traffic controllers walked off the job for three hours, forcing state Olympic Airlines to cancel 28 flights and reschedule another 14. State hospitals were operating with skeleton staff in a 24-hour strike.
The government appealed for calm after another teenager was shot in the hand late Wednesday near his school. It was unclear who shot him.
Police spokesman Panayiotis Stathis said no officers were in the area at the time of the attack, and Interior Minister Prokopis Pavlopoulos promised a thorough investigation. The boy underwent surgery Thursday.