The regime did not completely release the pressure on Douma however, the latest strikes killing at least 13 people overnight, the Syrian Observatory for Human Rights said.
The rebels said in a statement Friday that the agreement will allow humanitarian aid and medical care to be delivered to civilians in the area, who have lived through years of occupation and almost nonstop fighting as of late.
The Syrian Army, reportedly gained control of 90 per cent of the territory in Eastern Ghouta, considered the main opposition stronghold near Damascus, in a month-long government offensive to take the area.
Damascus and its ally Moscow have implemented a "leave or die" strategy with deadly air strikes on the enclave.
Once the government had whittled down rebel territory to three isolated pockets, it pursued separate evacuation deals with the factions present in each zone.
Thousands of fighters and their families departed the area by bus, according to an agreement between the Faylaq al-Rahman rebel group and Russian and Syrian authorities.
The fresh deal comes a day after the Failaq al-Rahman group declared a unilateral ceasefire to negotiate its withdrawal from the region.
Some have moved deeper into the rebel-held enclave, while 105,000 others have crossed the front lines toward government-controlled areas or left to rebel-held parts in northern Syria, according to state news agency SANA.
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"We unfortunately have a steady stream of reports coming out of Eastern Ghouta: of attacks of bombardments, all kinds of illegal weapons being used." said Jens Laerke, spokesman for the U.N. Office for the Coordination of Humanitarian Affairs (OCHA), during a news conference in Geneva. The first batch of fighters to quit Ghouta under a Russian-brokered deal were bused out on Thursday and started arriving in the northwestern province of Idlib on Friday.
Syrian forces have split Eastern Ghouta into three pockets, which are under the control of three different rebel groups.
Four major rebel groups are now positioned inside Eastern Ghouta, namely the Islam Army, Failaq al-Rahman, Ahrar al-Sham, and the Levant Liberation Committee, known as the al-Qaida-linked Nusra Front.
Retaking eastern Ghouta, a sprawling semi-rural area which had escaped regime control since 2012 and lies within mortar range of central Damascus, was made a priority by the regime this year.
The Observatory says that more than 1,600 civilians have been killed in just over a month. On Thursday, a total of 413 militants and 1,580 civilians, including 385 women and 576 children, left Harasta for Idlib.
A third part of the enclave, which includes the city of Douma in the north, is controlled by the Jaish al-Islam opposition group and is the last section under rebel influence.
The government's crushing offensive killed almost 1,500 people and wounded more than 5,000, according to opposition activists.