In exchange, five Hezbollah prisoners held by fighters from Jabhat al-Nusra -- which cut ties with al Qaeda when the group re-branded last year -- will be freed.
Jabhat al-Nusra, now known as Hayat Tahrir Al-Sham (HTS), and ISIS took over large swathes of the Lebanon-Syria border region in 2014.
Hezbollah, together with the Lebanese army, has waged a military campaign to recapture the territory. In recent weeks, Hezbollah says it has regained control of around 95% of the area, culminating in the ceasefire deal, which was agreed last week.
In the first phase of the ceasefire on Sunday, the Lebanese Red Cross said 15 of its ambulances shuttled the remains of militants across the border.
Around 150 buses were stationed at the Lebanese-Syrian border Monday to transport thousands of Syrians to the Syrian regions of Idlib and Qalamoun.
The prisoner swap was expected to take place in Aleppo, according to the Hezbollah's TV station Al Manar.
The UN refugee agency, which was not involved in the deal, expressed fears that the swaps would endanger civilians.
"UNHCR believes that conditions for refugees to return in safety and dignity are not yet in place in Syria," spokeswoman Lisa Abou Khaled told Reuters on Monday.
Khaled said the UNHCR has been trying to reach refugees in the border region of Arsal to determine whether returns were voluntary.
'Exceptional and well-planned defenses'
On Saturday, Hezbollah took journalists, including CNN reporters, on a tour of the mountainous area that it recaptured from HTS in recent days.
"The enemy was spread in the whole area. In terms of armament, they had everything. [Jabhat al-Nusra] had mortars, missiles and ammo. We used several kinds of maneuvers to liberate the area," a Hezbollah field commander said at a press briefing on site.
The unnamed commander praised the militant group's "exceptional and well-planned defenses."
In an address last week, Hezbollah Secretary General Hassan Nasrallah said the recaptured territory would be handed over to the Lebanese army "when the battle is over."
The Lebanese army has been primarily engaged in a fight against ISIS positions in the area of Ras Baalbek near the Syrian border.