Earlier, rioters used sledge hammers to smash the glass fronts of more than a dozen shops, banks and a cinema in the capital.
Police said at least nine suspected rioters were detained, while two officers were injured.
'No more sacrifices'
Thursday's strike shut down all public services and schools, leaving ferries tied up at port and suspending all news broadcasts for the day.
State hospitals were left with emergency staff as workers walked off the job for 24 hours to protest against spending cuts and tax hikes planned by George Papandreou, the Greek prime minister.
The GSEE and Adedy, its public-sector sister union, have said that the measures will hurt the poor and worsen the economy.
About half of the nation's five million workers are represented by the unions for the 24-hour strike.
Strikers and protesters banged drums and chanted slogans such as "no sacrifice for plutocracy," and "real jobs, higher pay".
People draped banners from apartment buildings reading: "No more sacrifices, war against war."
Some private bank branches were open despite calls from the bank employees' union to participate in the strike.
Barnaby Phillips, Al Jazeera's correspondent in Athens, said: He [Papandreou] is in a very tight spot, but there is perhaps a feeling ... that support for him is beginning to ebb, perhaps inevitably, as people begin to understand the details of this austerity programme and how it's going to hit them in their pockets.
"The latest opinion polls show most people are against many of the measures he is proposing and the main opposition party, New Democracy, has broken ranks with the centre-left party that is in power and is speaking against many of the policies.
"When you go out on the streets into the demonstrations people will tell you it's simply not fair that they are being targeted, they are going to have to pay for a mess which they did not create."
While their colleagues clashed with groups of protesters, some police joined the demonstration.
About 200 uniformed police, coast guard and fire brigade officers, who cannot go on strike but can hold protests, gathered at a square in the centre of Athens shortly before the marches got under way.
"The police and other security forces have been particularly hard hit by the new measures because our salaries are very low," said Yiannis Fanariotis, general secretary of one police association.
He said the average police officer made about $1,360 to $1,635 a month if weekend and night shifts were included.
Fanariotis said joining the protest "doesn't feel strange, because we are working people like everybody else and we are all shouting out for our rights".
Shopkeepers along the demonstration route scrambled to roll down their shutters for fear of violence, while a few blocks away, people sat at outdoor restaurants, nonchalantly continuing their meals.
Minor clashes also broke out in the northern city of Thessaloniki, where about 14,000 people marched through the centre.
The government says the tough cuts are the only way to dig Greece out of a crisis that has hammered the common European currency and inflated the loan-dependent country's borrowing costs.
|About 200 uniformed police joined the protests in Athens [AFP]
But unions say ordinary Greeks are being called to pay a disproportionate price for past fiscal mismanagement.
"They are trying to make workers pay the price for this crisis," said Yiannis Panagopoulos, the leader of the GSEE, Greece's largest union.
"These measures will not be effective and will throw the economy into deep freeze."
Fears of a Greek default have undermined the euro for all 16 countries that share the currency, putting the Greek government under intense European Union pressure to quickly show fiscal improvement.
It has announced an additional $6.5bn in savings through public sector salary cuts, pension freezes and consumer tax hikes to deal with its ballooning deficit.
The latest cutbacks, added to a previous $15.24bn of austerity measures, seek to reduce the country's budget deficit from 12.7 per cent of annual output to 8.7 per cent this year.
The long-term target is to bring overspending below the EU ceiling of 3 per cent of GDP in 2012.