The announcement follows months of security incidents in Syria which were blamed on Israel by Syrian officials but remained shrouded in mystery as Israel neither confirmed nor denied involvement.
Israel opposes Syria's new rulers, which hail in part from Sunni Muslim jihadist groups, despite their victory in a long civil war over the Iran-backed Assad dynasty.
"The IDF detained and transferred for interrogation operatives from several terrorist cells operated by Unit 840 - the Quds Force’s special operations unit," the Israeli Defense Force said in a statement.
"The terrorist cells were directed by the unit with the aim of carrying out terrorist attacks against the State of Israel," it added.
The United States and Arab states back the new authorities in Damascus as a bulwark against Iran and its Lebanese ally Hezbollah.
Sectarian clashes have blighted Syria's new era, and Israeli airstrikes on government buildings earlier this year signaled the Jewish state's growing opposition.
In the statement on Friday, Israel's military added that raids in March and April this year had detained two alleged Iran-backed operatives in Syria with Arabic names, and that Israeli attacks had assassinated two others in Lebanon last month.
"During the interrogations of the detained terrorists, it was revealed that some of them did not even know on whose behalf they were operating, and that many were recruited to Unit 840 without disclosure of the unit’s true motives and through financial bribes," it said.