"Seven hundred armed men with their personal weapons will leave Daraya to head to the (rebel-controlled) city of Idlib, while thousands of men and women with their families will be taken to reception centres," it said.
The rebels would have to surrender other armaments to the army.
A military source told AFP that the army would enter Daraya, which has been under a regime siege for the past four years, after the evacuation from the rebel-held town.
A rebel official in the town said the evacuation would begin on Friday, while a Syrian source on the ground said it would last four days.
"The civilians will go to regions under regime control around Damascus, rebels will go to Idlib "or sort out their situation with the regime", the rebel official said.
An opposition activist inside Daraya and a Syrian regime source late Thursday said that the town had been calm for the past 24 hours.
The rebels who control the town belong to two Islamist groups: Ajnad al-Sham and the Martyrs of Islam.
According pro-regime website almasdarnews, the army had advanced in recent days inside the town.
A convoy of trucks carrying food reached Daraya in June, delivering supplies to civilians for the first time since government forces laid siege to the town in late 2012.
Daraya was one of the first towns in Syria to erupt in anti-government protests. It is located just a 15-minute drive from central Damascus and is even closer to the regime's Mazzeh air base.