Under the terms of the agreement, militants who do not wish to reconcile with the state are being bused to northern Syria where they will join more than two million people, around half of them displaced from other areas, in the final zone of opposition control.
But fears for the rescue workers, who have often been targeted while racing to sites of government bombing, had been growing for weeks.
The Syrian Government views the group a "terrorist" organisation because it works in areas controlled by the country's armed opposition, and White Helmets have been pulled from buses by pro-government forces during previous evacuations of opposition-held territory before disappearing into the state's notorious network of prisons.
"It was an operation to rescue the rescuers," said one person with knowledge of the mission.
"They were in a terrible state. They'd been on the move for days, having to rely on really scant information. Even hours before they didn't know what was going to happen."
The unprecedented operation came perilously close to failure on multiple occasions through the night, sources with knowledge of the matter said.
An initial plan to leave through three separate crossings was scuppered when Isis forces took over one of the positions, leaving part of the group trapped and unable to reach the border. Their fate remained uncertain today.
Eventually, the rescue workers and their families - fragile and exhausted - crossed the Israeli border on foot as searchlights lit up the night sky. They were then bused through northern Israel to Jordan, where they were met by representatives of the United Nations refugee agency.
Still formally at war with Syria, Israel has periodically waded into the conflict to curtail Iran's growing influence in the region or deal with spillover from battles along its border. But despite international pleas, it has consistently pushed back against international pressure to take in refugees, even as neighbouring Lebanon, Jordan and Turkey have altogether accepted millions of Syrian civilians.
In a statement, Israeli Prime Minister Benjamin Netanyahu said he had been approached by US President Donald Trump, Canadian Prime Minister Justin Trudeau and several other world leaders, and asked for help evacuating White Helmets in "mortal danger."
"At the same time, we are not ceasing to act in Syria against Iran's military buildup there," he said.
After seven years of civil war, the Syrian Government forces are back in control of most of the country and the battle against rebel groups is almost over.
In Syrian state media, the dramatic rescue mission was framed as part of an international conspiracy, highlighting the group's Western funding and saying that countries involved in the mission had given safe passage to "terrorists" from Syrian soil.
In a joint statement, British Foreign Secretary Jeremy Hunt and International Development Secretary Penny Mordaunt paid tribute to the rescue workers' "brave and selfless work" and said that the White Helmets was believed to have saved more than 100,000 lives during the course of Syria's war.
"We judged that, in these particular circumstances, the volunteers required immediate protection," the pair said.
