The deaths came in clashes that began on Tuesday when two prominent rebel groups launched simultaneous attacks on three areas outside the capital.
The Jaish al-Islam and Faylaq al-Sham attacks have focused on the areas of Harasta, Dahiyat al-Assad and the region around Adra prison, the monitor said.
"Clashes since September 8 have killed 46 rebels," said Observatory chief Rami Abdel Rahman.
On Wednesday, Jaish al-Islam also began an assault on Adra prison, Syria's largest prison and where. It briefly captured two buildings in the women's section of the prison, but was subsequently forced back.
In Damascus city meanwhile, the Observatory said one person had been killed and 10 wounded in rebel fire on the Bab Tuma district.
Rebel forces including Jaish al-Islam regularly fire rockets into Damascus from rear bases on the city's outskirts.
The government frequently carries out deadly air strikes on the rebel-held areas outside Damascus, often killing dozens of terrorists at a time.
More than 240,000 people have been killed in Syria since the conflict began in March 2011.