According to military bodies, the military previously rejected a proposal by the Daesh extremists to leave for the northern province of Raqqa and told them to immediately surrender.
Coinciding with the military operation, Lebanese group Hezbollah also announced that its fighters, along with Syrian regime forces, had begun an onslaught to recapture the outskirts of Qalamoun from Daesh in western Syria.
The group's War Media channel said the unilateral pause was "in the framework of a comprehensive agreement to end the battle in west Qalamun against Daesh (IS)".
Both offensives have advanced towards the border from opposite sides.
The Lebanese army command said the fourth phase of the offensive that began on Saturday should eventually evict all IS fighters from the border region.
Lebanese army declares ceasefire that comes into affect in a Daesh pocket straddling the Syria-Lebanon border, to decide the fate of nine of its soldiers who were abducted by Daesh in August 2014.
"The remaining ISIS terrorists are completely confused and seek an escape or any settlement to exit the area which they have occupied after being besieged", he said in a statement reported by the Syrian Arab News Agency.More news: Super-subs guide Manchester United past Leicester City
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Sixty-two Lebanese soldiers have been killed by ISIL or Syria's former Al Qaeda affiliate in and around Arsal since 2013, the Lebanese army spokesman said.
In a speech Thursday, meanwhile, Hezbollah leader Hassan Nasrallah said that ISIS had been defeated, but that authorities were still negotiating to find out the fate of the missing soldiers.
If Lebanon wanted to negotiate for IS to evacuate its territory, he said, the Syrian government would be ready to accept any formal request from Beirut.
Nusra militants and a Syrian rebel group withdrew from Lebanon's border region earlier this month. The province is southeast of Raqqa, where the U.S-backed Syrian opposition forces are battling ISIS militants.
Hezbollah has been fighting alongside troops loyal to President Bashar al-Assad since the Syrian conflict erupted in 2011.
Last week, Lebanon and Hezbollah each announced they had made significant gains against ISIL fighters, driving them back into a smaller part of the arid hills on the border.
"We see no evidence of substantive cooperation (between the army and Hizballah)", the diplomat added.