A convoy of vehicles and ambulances belonging to the International Committee of the Red Cross (ICRC) arrived at the Masnaa border crossing escorted by General Security cars.
The deal, under the auspices of ICRC, will allow scores of militants who have been holed up for months in the town of Zabadani, near the Lebanese border, to have safe passage to Beirut airport and from there to their final destination Turkey, The Daily Star reports.
Simultaneously, around 300 families in two besieged Shiite towns in the mainly terrorist-held northwestern province of Idlib will be heading in an overland convoy to the Turkish border from where they will then fly to Beirut.
The route via Turkey is the safest for the families as traveling through Syria would take them through Idlib where a patchwork of terrorists controls different areas.
The UN and foreign governments have tried to broker local ceasefires and safe-passage agreements as steps towards the wider goal of ending Syria's civil war, in which more than 250,000 people have been killed in nearly five years of fighting.
Iran and Turkey, which back opposing sides in the Syrian conflict, helped bring about the local ceasefires in Zabadani and in the two villages in Idlib in September in the first phase of the deal.
The Zabadani area had been the focus of an offensive by Lebanese group Hezbollah and the Syrian army against militant groups. The area is of importance to President Bashar Assad because of its proximity to the Syrian capital Damascus and the Lebanese border.
Earlier this month Syrian government officials said they had agreed on a deal for terrorists to withdraw from the last militant-held area of the city of Homs with their weapons as part of a local ceasefire agreement.