About 150 people had gathered near the interior ministry, demanding the release of political prisoners.
It follows Tuesday's "day of rage" when hundreds calling for democracy protested in Damascus and Aleppo.
The interior ministry said "infiltrators" tried to stir chaos. But among those held was a 10-year-old boy.
Activists say he was with his father - and both were detained.
Others included 69-year-old Damascus university philosophy professor and author Tayeb Tizini, and leading human rights activist Suhair Atassi.
"They pulled Suhair by her hair and took her away," one demonstrator said, according to Reuters.
Journalist and activist Mazen Darwish told the BBC that he was set free only after being held for five hours in the military security branch's detention centre alongside 20 others, including women. A further 15 were still being detained by state security, he said.
"When I showed them my international press card they shouted and said 'Why were you standing among protesters and not among the journalists?'," said Mr Darwish, head of the Syrian Centre for Freedom of Speech.
No further information about those detained was immediately available.
No dissent
The ruling Baath party has dominated Syrian politics for nearly 50 years.
President Bashar al-Assad - who came to power in 2000 after three decades of rule by his father Hafez - has moved slowly to open up the economy, but his administration does not tolerate any dissent.
Some of the 150 protesters who gathered held photos of those they said had been imprisoned for their political views.
"After a long wait and rumours of an impending release of prisoners of conscience in Syria, our hopes have vanished," said a statement from the Syrian Observatory for Human Rights.
The organisation - which groups together the families of 21 jailed human rights activists - had said it planned to demonstrate in front of the ministry on Wednesday.
Reports said that shortly after the protesters gathered a counter-demonstration was held in the same square with people chanting that they would defend the Syrian president "with our soul, with our blood".
The interior ministry denied that the initial protest was political in nature.
"There were some persons who took advantage of this call to slip among these people and tried to shout some slogans," said Gen Mohamed Hassan al-Ali, of the interior ministry's moral guidance department.
There are thousands of political prisoners in Syrian jails, and major opposition groups are banned.
The government also blocks access to several internet sites and maintains strict control of the media though authorities have lifted bans on Facebook and YouTube in the wake of uprisings in Tunisia and Egypt.
In January, President Assad told the Wall Street Journal that Syria was more stable than Tunisia and Egypt. He said that there was no chance of political upheaval, and pledged to press on with a package of reforms.
The BBC's Lina Sinjab, in Damascus, said that many had doubted that any protests would take place in Syria, but observers here believe events over the past couple of days have broken the silence that dominated the country.
At least 35 people have been arrested after they defied a ban on demonstrations and protested in the Syrian capital, reports say.