'The civilians were evacuated from the war zone in southern Syria due to an immediate threat to their lives.
The agricultural area has become the main battleground in the sensitive border region after a major Russian-backed Syrian army offensive routed other rebel groups who were once backed by Washington, Jordan and Gulf states.
The Israeli 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.
The Syrian government managed to get full control over a strategic territory at the border with Jordan following the operation.
Since the Syrian government offensive began in June, the area along the frontier with the Golan Heights has been the safest in the southwestern region, attracting hundreds of displaced people because it is along the disengagement line with Israel demarcated in 1974 after a war.
The government and Russian Federation view the White Helmets as "agents" of foreign powers and have regularly accused them of staging rescue missions or chemical attacks.
The United Nations helped with the evacuation through the Golan Heights.
"Following an Israeli government directive and at the request of the United States and additional European countries, the IDF recently completed a humanitarian effort to rescue members of a Syrian civil organisation and their families", said the Israel Defence Forces.
The rescue marked the first time in the eight-year war that Israel has allowed Syrians to flee through its territory.
The White Helmets have rescued thousands of civilians caught up in fighting in opposition-held zones along various fronts of Syria's seven-year conflict.
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. This has left civilians stranded between the Israeli-held Golan Heights and Jordan.
The Syrian army said its aerial strikes and shelling of militants in the Yarmouk Basin - the only territorial pocket held by the hardline Sunni fundamentalists in the country's southwest - had killed "tens of terrorists" in a campaign whose goal it said was to crush militants. The Observatory said two buses carrying evacuees were held up by a pro-Syrian government militia, apparently after they went off road.
Mr Kayed said those relocated would stay in "a restricted area" of Jordan until they are dispersed to the three countries within three months.