The violence involved about 200 youths who hurled firebombs and rocks at riot police, and smashed office windows and set fire to trash bins.
Many of the mask-wearing protesters carried wooden bats and pieces of smashed paving stones, in the worst clashes seen since Prime Minister Alexis Tsipras' left-wing government was formed six months ago.
The clashes died down as a debate got underway in parliament on a new austerity bill.
Earlier, more than 10,000 people, supporters of left-wing groups and a Communist-backed trade union, staged a peaceful rally in central Athens.
Meanwhile, Germany says the idea that basic human rights in Greece might suffer because of austerity imposed by the country's creditors is "fanciful."
Juan Pablo Bohoslavsky, an independent U.N. expert on foreign debt, says Greece's creditors may break international law if the conditions they impose on Athens lead to undue hardship.
Greece has seen drastic cuts to public services and a rise in unemployment and homelessness because of austerity measures introduced in recent years.
German Finance Ministry spokesman Martin Jaeger said Wednesday that he couldn't see evidence of human rights being ignored by Berlin.
Jaeger declined to say whether German officials had made or are making any attempt to ensure the demands on Greece are compatible with human rights law.