"The Daraya file is now closed after the evacuation of all the civilians, armed men and their families under the agreement" reached on Thursday between the regime and rebels, Syrian state television said.
It broadcast footage of army vehicles combing the streets of the town, one of the first to rise up against the regime in Syria's five-year-old revolt.
"The second and final convoy of rebels and civilians came out of Daraya today," said Rami Abdel Rahman, head of the Britain-based Observatory monitoring group.
The total number of evacuees was not immediately clear.
The official SANA news agency reported that 4,000 civilians were to be directed to reception centres and at least 700 rebels escorted to the rebel-held city of Idlib in northwest Syrian.
At least five buses carrying fighters and their families arrived in Idlib, the Observatory said.
The arrivals were the first since the evacuation of the town just outside Damascus began on Friday under the withdrawal agreement.
Daraya had been ravaged by constant army bombardment, and only a single aid convoy, last June, reached the town since it came under siege in late 2012.
Civilian residents of the town, believed to number around 8,000, have been taken to government-run reception centres pending resettlement.
- 'Survived on grass' -
A Beirut-based television, Al-Mayadeen, aired footage of soldiers taking pictures with their mobiles of buses loaded with rebels, who were allowed to keep their personal weapons under the deal.
"With our blood and our souls, we sacrifice ourselves for you, O Bashar!" soldiers chanted of President Bashar al-Assad as the buses drove by.
Inside the vehicles the rebels remained mostly impassive, although some responded by making the victory sign behind the windows.
Some 300 fighters and their families were evacuated during the first part of the operation on Friday, according to a military source.
While they were taken to Idlib, many of the evacuated civilians were transferred to Hrajela, 20 kilometres (12 miles) southeast of Daraya.
On Saturday, the evacuees spoke of years under siege in Daraya as children had their first taste of treats such as ice cream -- and tomatoes.
"My children, who are three and five, were very surprised to see tomatoes. It was the first time for them," said 30-year-old Houda.
"All we had to survive on was grass."
At the entrance to the reception centre in Hrajela, children played under a blazing sun as Red Crescent volunteers distributed mattresses, blankets and food.
Daraya, a drive of just 15 minutes from Damascus, became a symbol of the uprising which started with mass protests.
The rebels said they were forced to agree to evacuate the town because of deteriorating humanitarian conditions.
Anti-regime activists have condemned what they called the forced displacement of Daraya's inhabitants.
Long sieges have prompted rebels in several locations to agree evacuation deals with the regime, prompting activists to accuse Damascus of using "starve or surrender" tactics.
Rebel fighters pulled out of Syria's third city Homs last year under a similar evacuation deal to the Daraya agreement.
More than 290,000 people have been killed and over half the population displaced since Syria's conflict erupted in March 2011.