Past deals have mostly affected Sunni Muslims living in former rebel-held areas surrounded by government forces and their allies after years of sieges that have in some cases led to starvation.
Surrounded and bombed by hostile factions, the towns had become a rallying cry for the regime and its ally Iran.
The evacuation agreement reached Tuesday is not the first for the two tiny towns.
On Wednesday, barricades were lifted on the road leading into Fuaa and Kafraya, allowing 84 buses to enter, an AFP correspondent 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 fighters stood on the roadside as the convoy of evacuees inched past, with pro-government militiamen and regular civilians sitting solemnly on board and staring ahead.
A source from HTS on Tuesday said some 6,900 people - including civilians and fighters - were to be evacuated under the deal.
"As the buses entered regime-held areas, the regime started releasing detainees, as per the deal", Observatory chief Rami Abdel Rahman said.
Ambulances reportedly transporting prisoners realeased from government jails.
Buses had begun evacuating fighters and civilians early Thursday morning under a deal between regime backer Russian Federation and rebel ally Turkey to allow thousands to leave after three years of encirclement.
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"Over 1,500 civilian and rebel prisoners held in regime prisons will be released", said an opposition source familiar with the talks told Reuters. HTS said the area would be declared a military zone and, after inspections were completed, would be open for resettlement by refugees fleeing other parts of Syria.
The towns of some 20,000 people have been under siege since 2013.
The four towns also saw coordinated evacuation deals.
In April 2017, thousands were bussed out Fuaa and Kafraya in exchange for parallel evacuations from two towns near Damascus that were being besieged by the government.
But a blast targeting a convoy of evacuees from Al-Foua and Kafraya left 150 people dead, majority 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 northwestern province borders Turkey to the northwest but is otherwise nearly totally surrounded by regime territory.
The people of Kafraya and Foa had rejected a previous deal for their evacuation last April as they had received no strong guarantees of their safety after a similar deal was implemented a year ago and largely failed.
The conflict in Syria, which began in 2011, has left more than 350,000 people dead, and has now been raging longer than World War Two. The momentum in the seven-year war is now decidedly in Assad's favour, but large parts of the country's east and north remain outside of the regime's control, in the hands of American-backed Kurdish militias and Turkish-backed proxy fighters.
But with the progress of the Syrian army across the country, those sieges were broken by both sides, the latest of which was the government siege on the Eastern Ghouta countryside of the capital Damascus.