The refugees and fighters from al-Qaeda’s former Syrian branch arrived in bus convoys into the rebel-held area of Al-Saan in the central Syrian Hama province.
In return, Fateh al-Sham Front released five fighters from Syria regime ally Hizballah.
The swap was part of a broader ceasefire deal announced last week between the two sides which ended six days of fighting in the mountainous Jurud Arsal region in the restive border area between Lebanon and Syria.
“The operation is now over,” Rami Abdel Rahman, from the Syrian Observatory for Human Rights monitoring group said.
“All five convoys of buses carrying fighters from Fateh al-Sham Front and (Syrian) civilians have reached the area” in central Hama province, he added.
As each convoy reached its destination, the group – once known as al-Nusra Front and later as Fateh al-Sham Front – released one Hizballah fighter, the Lebanese movement’s War Media said.
The five fighters had reportedly been captured by the former al-Qaeda affiliate during clashes in Aleppo province.
The fighters and the civilians were later seen getting off the buses and boarding others vehicles belonging to local humanitarian organisations for an unknown destination.
Relief workers handed out water bottles and food to the evacuees, an AFP correspondent said.
On Wednesday, a total of 7,777 people – mostly civilians – were evacuated from Jurud Arsal in line with the ceasefire. Under the deal – which also calls for the release of three detainees from a Lebanon prison – the bodies of nine Syrian fighters were swapped for the remains of five Hizballah fighters.
Tens of thousands of Syrian refugees live in the town of Arsal, adjacent to the border region, and an unknown number are also thought to have taken shelter in the surrounding mountains. More than one million Syrians are registered with the United Nations as refugees in Lebanon, a country of just four million people.