It was the first such Israeli intervention in Syria's lengthy civil war, now in its eight year.
"The civilians were evacuated from the war zone in southern Syria due to an immediate threat to their lives", the IDF said on its Twitter account, describing the move as "an exceptional humanitarian gesture".
Israel has assisted the evacuation of 422 Syrians - including members of the White Helmets rescue group - to neighboring Jordan in an worldwide humanitarian operation coordinated by the United Nations.
'The government gave the permission after Britain, Germany and Canada made a legally binding undertaking to resettle them within a specified period of time due to "a risk to their lives",' it explained.
Jordan's Foreign Ministry confirmed that it had allowed 800 Syrian citizens to enter the country and said they would travel on to Britain, Germany and Canada within three months.
The White Helmets confirmed in a tweet Sunday that volunteers and their families were evacuated to Jordan for "purely humanitarian" reasons after becoming "trapped in a risky area".
The military said its actions did not reflect a change to Israel's non-intervention policy in Syria's war, where all the warring parties are considered hostile.
Supporters of Syrian President Bashar al-Assad, and his Russian allies, say the White Helmets support the rebels and also have links to jihadist groups.
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Through videos, pictures, and social media, the White Helmets are widely seen as having played an important role in showing the worldwide community the horrors of the Syrian civil war.
The Syrian regime launched a large offensive in June that has retaken the rebel-held areas in Dara'a and Quneitra bordering Jordan and the Golan.
Israel at the weekend played a critical role in rescuing hundreds of humanitarian workers and their families trapped in southern Syria.
The Syrian government is unlikely to fire there or carry out airstrikes for fear of an Israeli response.
A former resident in touch with relatives said thousands of civilians had fled bombed villages to areas held by the army or the rebels.
More than 650,000 Syrian refugees are registered with the UN High Commissioner for Refugees (UNHCR) in Jordan but the kingdom says it hosts 1.3 million Syrian refugees.
German weekly magazine Bild, which broke news of the evacuation and published footage of buses used to transport the Syrians across Golan, said 50 of them would be granted asylum by Berlin.
Last week, Israel delivered 72 tons of food, approximately 70 tents, 9,000 liters of fuel, as well as pallets of medicine, medical equipment, clothing and children's toys as part of six special operations in several locations in south west Syria.