At least 23 bodies, including those of women and children, were discovered in the eastern suburb of Zamalka on Thursday, while another 22 were found in Qatana in the countryside southeast of the capital, the Syrian Observatory for Human Rights said.
Zamalka has been a hotbed of anti-government protests, sparking repeated raids by the army and clashes with rebel fighters.
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Opposition activists blamed pro-government forces for the killings in the town, accusing President Bashar al-Assad's regime of a "new massacre."
The Observatory also reported that two kidnapped brothers of a Syrian rebel commander were killed on Thursday.
The men were seized at an army checkpoint on Wednesday night, it said. They were found dead in the Qadam district of Damascus amid a sharp increase in reports of abductions across the country.
Amateur video posted on YouTube by activists showed the bodies of the two men, identified as Mohammed and Ahmed al-Zakh, covered in blood. The head of one of the victims had been partly blown off.
The Observatory said that nationwide a total of 131 people were killed on Thursday -- 65 civilians, 24 rebels and 42 soldiers.
Early on Friday, two children were killed in shelling in the town of Albu Kamal on the Iraqi border while two rebel fighters were killed by mortar fire in the eastern city of Deir Ezzor, the Britain-based watchdog said.
A raid by security forces on the Al-Qazzaz district of southeast Damascus, in which troops rounded up dozens of suspected militants, sparked clashes with rebel fighters, it added.
Gunfire was also heard from the Tadamun district in the southern suburbs of the capital and the Yarmuk Palestinian refugee camp.
