According to the agreement, Jaish al-Islam fighters will leave Douma for the northern city of Jarablus, near the borders with Turkey, within 48 hours.
The Syrian government said it would start negotiations on Sunday with the rebel group Jaish al-Islam.
Deadly air strikes slammed into the last opposition-held town in Syria's Eastern Ghouta on Friday.
The Syrian rebel group Jaish al-Islam said on Friday it had agreed to evacuate Nusra Front fighters being held in its prisons.
The two major rebel factions in Syria's eastern Ghouta welcomed on Saturday a U.N. resolution demanding a 30-day truce.