A total of 71 buses carrying hundreds of militants and their families departed toward rebel-held areas in northern Syria, according to the state news agency SANA.
The militants were thoroughly scrutinized and their name list was double checked ahead of their departure, said SANA, adding that the evacuees have handed over their weapons.
SANA said the militants have detonated their positions in the Rastan area in the northern countryside of Homs ahead of their departure.
The third batch was supposed to evacuate on Wednesday toward the province of Idlib and the northern city of Jarablus, but the rebels in those areas have hurdled the entry of the first two batches from Homs and Hama.
The evacuation deal was reached between the rebels and the Syrian government on May 1 under the mediation of Russia and is identical to other agreements that have been recently reached in the capital Damascus, which saw the evacuation of rebels from the Eastern Ghouta countryside and the eastern part of the Qalamoun region to Idlib and Jarablus last month.
The Russian-backed evacuation deals aim at curbing battles. Meanwhile, the rebels are leaving for other strongholds in northern Syria in order to secure more vital areas in central and southern Syria.