Israel said its air defences fired at rockets that approached territory under its control from Syria on Monday, where regime troops are taking control of areas bordering the Israeli-occupied Golan Heights.
It also also tweeted that the "civilians were subsequently transferred to a neighbouring country".
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.
A documentary short about the group won an Oscar in 2017.
Israel seized 1,200 square kilometres of the Golan from Syria in the 1967 Six Day war, in a move never recognised by the worldwide community.
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. The Israeli military declined comment.
Its activation came after Israel on two separate occasions this month fired Patriot missiles at incoming drones from Syria.
An Israeli source briefed on the David's Sling activation said the interceptor missiles were launched following an initial assessment that the two incoming Syrian SS-21 rockets would hit the Israeli side of the Golan.
"Several days ago President Trump contacted me, as did Canadian Prime Minister [Justin] Trudeau, and others, and requested that we assist in evacuating hundreds of "white helmets" from Syria".
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Earlier, the Green Shirts won T20 tri-series after beating Australia and the hosts Zimbabwe . Prince Masvaure (39) and Murray also got starts before both fell while going for big shots.
The meeting was requested by Russian President Vladimir Putin, Netanyahu said earlier in the day.
Netanyahu and Putin have held a number of discussions in recent months on the Syrian conflict and Iran's military presence there, which Israel opposes.
More than 400 rescue workers and family members from Syria's southern provinces of Daraa and Quneitra were ferried into Israel on Sunday, then taken into Jordan for resettlement into Western countries.
State news agency SANA, citing a foreign ministry official, said the evacuation "exposed the true nature of the organisation known as the White Helmets", calling it a risk to stability and security "because of its terrorist nature".
For years the volunteers, officially called the Syria Civil Defense and famous for their white hard hats, have rushed to save civilians trapped in the rubble caused by airstrikes from Syrian warplanes.
The White Helmets is a network of first responders which rescues the wounded in the aftermath of air strikes, shelling, or explosions in rebel territory across Syria.
"We thank all governments who contributed to the success of this operation to rescue the rescuers, and we ask that they do more to help the hundreds of thousands remaining in southern Syria", they said.
"Israel has always claimed that it has nothing to do with the ongoing war against Syria, but the smuggling of hundreds from the terrorist White Helmets organization and leaders of other armed terrorist organizations-in cooperation with the governments of the United States, Britain, Jordan, Germany and Canada-reveals the support presented by these countries to terrorist groups in their aggression against Syrians and their destruction of infrastructure in Syria under false pretenses", a ministry official was quoted as saying by Syria's state television.