More than 100 buses arrived on Wednesday to transport residents and fighters overnight from the villages to nearby government-held territory in Aleppo province.
Several thousand residents were evacuated from two pro-regime towns in northern Syria on Wednesday, ending one of the longest sieges of the country's civil war, now in its eighth year.
Fuaa and Kafraya in Idlib province were the last remaining areas under blockade in Syria and a rare example of pro-regime towns surrounded by rebel forces.
The Shia-majority towns were besieged for three years by rebels and Hayat Tahrir al-Sham (HTS), a Daesh alliance led by Syria's former Al-Qaeda affiliate.
Surrounded and bombed by hostile factions, the towns had become a rallying cry for the regime and its ally Iran.
A deal was reached on Tuesday between regime-backer Russia and opposition-ally Turkey to see the residents taken to regime-held territory in exchange for the release of prisoners from regime jails.
On Wednesday morning, barricades on the road leading into the towns were removed to let dozens of buses in, AFP's correspondent there said.
Just after midnight, the buses drove out of Fuaa and Kafraya and Thursday morning were at the village of Al Eis, crossing from rebel-controlled territory into regime-held areas in Aleppo province.
Armed HTS militants stood on the roadside as the convoy of evacuees inched past, with pro-regime militiamen and regular civilians sitting solemnly on board and staring ahead.
Some 7,000 civilians and fighters were evacuated and the two towns were now "entirely empty of residents," the Syrian Observatory for Human Rights (SOHR), a Britain-based monitoring group, said on Thursday morning.
"As the buses entered regime-held areas, the regime started releasing detainees, as per the deal," SOHR chief Rami Abdel Rahman said.
According to HTS sources, the evacuation had been agreed in exchange for the release of 1,500 people from regime-run jails.
An HTS source said the group's fighters had entered the towns after the evacuation was complete.
Fuaa and Kafraya came under siege in 2015 as rebels overran the surrounding province of Idlib, cutting off access to food and medicine.
Those forces had allowed the United Nations and the Syrian Arab Red Crescent to deliver aid to the towns in exchange for similar deliveries to two regime-besieged towns near Damascus.
The four towns also saw coordinated evacuation deals.
In April 2017, thousands were bussed out of Fuaa and Kafraya in exchange for parallel evacuations from the towns of Zabadani and Madaya.
But a blast targeting a convoy of evacuees from Fuaa and Kafraya left 150 people dead, most of them civilians and including 72 children.
Some reports have suggested Tuesday's deal also involves an agreement to spare Idlib a military offensive by the regime.
The province borders Turkey to the northwest but is otherwise almost completely surrounded by regime-held territory.
It is home to more than two million people, including Syrian civilians and rebels moved out of other opposition-held territory in surrender deals.
Syria's conflict erupted in March 2011 with protests against Bashar al Assad that escalated into a devastating, complex war.
After losing swathes of territory to rebels in the early years of the conflict, Assad's forces have managed to regain much of the country since Russian forces intervened in the regime's favour in 2015.
The retaking of second city Aleppo last year marked a major turning point and earlier this year the regime retook Eastern Ghouta, the last rebel-held area near the capital Damascus.
Both victories followed crushing regime sieges and heavy bombardment.
In recent weeks Russia brokered a deal for rebels to hand over large parts of the southern province of Daraa, considered by many as the birthplace of the anti-Assad revolution.
Fighting has continued in the south though, with at least 15 civilians reported killed in air strikes in Daraa province on Wednesday.