Haitham al-Maleh, an activist and lawyer, told Al Jazeera on Friday that protesters were close to Abasyeen Square when the intelligence services brought several buses carrying men with "pistols and sticks" who attacked protesters. He said those injured were taken away by medics.
Other sources said security forces used tear gas to disperse the crowds.
"I counted 15 mukhabarat [secret police] busloads. They went into the alleyways just north of the square chasing protesters and yelling 'you pimps, you infiltrators, you want freedom? we will give it to you'," a witness told Reuters news agency.
Elsewhere in the capital, violence reportedly erupted when dozens of armed men in plain clothes surrounded about 250 protesters rallying in front of the Salam mosque in Barzeh district.
Thousands were also demonstrating in the southern city of Daraa. Al Jazeera's Rula Amin said security forces were not visible in the city, and that the protesters were being allowed to hold their demonstration.
"It's a completely different scene from last Friday when more than 26 people were killed during protests and clashes with the security forces and protesters here. People went out after Friday prayers ... in thousands. They were marching carrying olive branches saying 'peaceful, freedom'. Some were demanding the toppling of the regime, others were saying they just want reforms," she reported.
"It comes one day after a delegation from Daraa met with President Assad in an attempt by the government to calm the situation. Now here in Daraa, these measures seem to have calmed the situation a little bit. People say the president promised them very specific reforms that will be announced very soon, maybe as early as next week."
Protests were also held in Baniyas, Latakia, Baida and Homs, but no clashes were reported there.
In the coastal city of Baniyas about 1,500 people chanted "freedom" after Friday prayers, despite the deployment of the army to contain protests, the Syrian Observatory for Human Rights said.
Rallies were also reported in the city of Deir ez-Zor, on the Euphrates river, and in Qamishli in the mainly Kurdish northeast.
Some of the protesters are calling for reform and an end to corruption, while others are calling for a complete regime change.