Earlier, Israel launched two David's Sling interceptor missiles at rockets which it said crashed inside Syrian territory and were part of the internal fighting there.
A documentary short about the group won an Oscar in 2017.
The announcement marks the first such Israeli intervention in Syria's civil war.
Russian Federation and Iran have backed the Syrian President Bashar al-Assad's government throughout the war, which started with a crackdown on protests in 2011 and has killed more than 400,000 people and displaced 11 million others.
Regime forces have now regained control of most of the two provinces through a combination of deadly bombardment and Moscow-brokered surrender deals.
The report did not elaborate on what exactly had been targeted, but an intelligence source told Reuters that a major military research centre for chemical arms production was located near the city and believed to house a team of Iranian military experts involved in weapons production.
On Sunday, 422 of the group and their family members arrived in Jordan, Jordan's foreign ministry announced.
Iran is Israel's main enemy and Netanyahu has long pushed for a tougher stand against it by global powers.
"Several days ago, U.S. President Trump contacted me, as did Canadian Prime Minister Trudeau and others, and requested that we assist in evacuating hundreds of White Helmets from Syria", Netanyahu said in Hebrew during an online address.
The foreign ministry in Damascus condemned on Monday the evacuation of hundreds of trapped White Helmets rescue workers and their relatives from Syria's south through its arch-foe and neighbour, Israel.
The Israeli military said Sunday it had rescued members of a Syrian volunteer civil organization from the volatile frontier area and evacuated them to a third country, the first such Israeli intervention in Syria's lengthy civil war.
A non-Jordanian source familiar with the agreement told Reuters news agency the original plan had been to evacuate 800 people, but only 422 made it out as operations were hampered by government checkpoints and the expansion of Islamic State in the area.
It noted that the White Helmets organization's activities were on territories controlled by extremists and staged fake scenes in order to be used as pretexts for making accusations against the Syrian army.
The White Helmets typically have operated in opposition-held areas across Syria, places where government services are nearly non-existent, voluntarily risking their lives to save hundreds of civilian lives during relentless government airstrikes and bombardments.
Prime Minister Benyamin Netanyahu initially pushed for a 40 kilometer-wide no-go zone for Iranian militias and the Quds Force of the Iranian Revolutionary Guards Corps on the Syrian side of the Golan Heights but failed to enlist Russian president Vladimir Putin for his political offensive against the Iranian presence in Syria.
Writing on Twitter in Arabic, Jordanian Foreign Minister Ayman Safadi said the Syrians were allowed into the country following written commitments that Germany, Britain and Canada would resettle them following the operation.