On June 19, Syrian government forces launched a Russia-backed offensive to retake Daraa and Quneitra provinces.
Regime forces had increased their offensive in the area in recent weeks, making the rescue effort even more urgent.
In a statement, the Israeli military said it had completed "a humanitarian effort to rescue members of a Syrian civil organization and their families ... due to an immediate threat to their lives".
Despite the intervention, the IDF said that "Israel continues to maintain a non-intervention policy regarding the Syrian conflict".
Hundreds of Syrian rescue workers from the United States-backed White Helmets group have been evacuated through Israel into Jordan, escaping an onslaught by the regime of Syrian president Bashar al-Assad on one of the last opposition strongholds in the country.
The informed source close to the operation told NPR that only 422 people actually made it out of the country, because of heavy fighting on the ground.
Israel has not given an exact number of evacuees.
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.
Rescue workers known as the White Helmets are expected to be resettled in Britain after an evacuation from Syria's conflict-scarred southern border. They were besieged in a very unsafe area.
The group are now in Jordan where they have been given temporary asylum.
The White Helmets work exclusively in rebel-held areas and receive donations from several Western governments, including Britain, Germany, the Netherlands, and the United States.
Last year, a Netflix production called The White Helmets won an Academy Award for the best short documentary.
The White Helmets were taken across the border and then ferried on buses across the Israeli-occupied Golan Heights and on into Jordan.
The group, which operates in opposition-held areas, is often targeted in Syrian government attacks on its members and facilities.
The organisation has been told that it was a one-time evacuation, but its members are lobbying for more to be allowed to escape the regime advances.
Netanyahu said Trump, Canadian Prime Minister Justin Trudeau and others had spoken to him recently asking for help in extracting the White Helmets.
Massive Israeli airstrikes on Hamas positions in Gaza on Friday after the death of a soldier on the border were seen as key to the terror group requesting a ceasefire.
"The request was approved based on pure humanitarian reasons", he added.
Canada will take in up to 50 White Helmets volunteers and their families, totalling up to 250 people, officials said.