Some marchers attacked riot police with rocks, flares, firebombs and paint, only for the officers to respond with tear gas.
At least 60,000 people attended the demonstrations which left around 10 police officers injured.
Some protesters jumped over a barrier and attempted to climb up the steps of the Greek parliament but were chased down by police officers.
One man draped in a Greek flag attacked police with a large stick, while others beat nearby officers with big flags on wooden poles.
A statement from Greek prime minister Alexis Tsipras blamed “extremist elements and members of Golden Dawn”, an extreme right party, for the unrest.
“In our democracy, citizens’ free expression is an inalienable right, even for those who want to abolish democracy,” the statement said.
“It is also the duty and obligation of those of us who do believe not to allow them. Let’s isolate and condemn them.”
Macedonia and Greece struck a deal in June to end a decades-long dispute over Macedonia’s name.
The country will now be called North Macedonia but the protesters believe the name is a usurpation of ancient Greek heritage and implies territorial claims on Greece.
Away from Athens, farmers in northern Greece temporarily blocked the highway leading to the Macedonian border, in a show of solidarity. It later reopened.
Additional reporting by agencies
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