IDF soldiers rappelled from four helicopters to a military post near Kiswa, south of Damascus, a Syrian military source told Al Jazeera on Wednesday.
Dozens of soldiers carrying search equipment carried out the operation, which lasted over two hours.
There were no reports of clashes between the IDF and the Syrian military during the operation.
This comes after reports broadcast by state-run Al Ekhbariya TV cited two Syrian army sources claiming that Israel launched a series of strikes on a former army barracks in Kiswa.
Iran had used the air defense base during the rule of the ousted Syrian leader, Bashar al-Assad. Locations of earlier strikes - in the Kiswa region and the strategic Jabal Manea hilltop - were also among the most significant military outposts used by pro-Iranian terror groups during the Assad era.
Asked for comment on the strikes, an Israeli military spokesperson said: "We do not comment on foreign reports."
On Thursday morning, Defense Minister Israel Katz made a statement on X/Twitter, not necessarily confirming the reports, saying, "Our forces are operating on all fronts, day and night, for the security of Israel.
A non-final estimate from Syria's Shams TV claimed that nine soldiers were killed and others wounded in Israeli airstrikes on the Kiswa area in the Damascus countryside.
Israel has stepped up incursions into southern Syria, and the latest strikes coincided with security talks between Damascus and its long-time adversary aimed at reducing tensions.
Assad's army may have left equipment behind, possibly from Iran
Another military source said Syria believes equipment was left behind in the area, perhaps by Iranian-backed terror groups that were entrenched there. The new Syrian army has since established a token presence there.
The source added that there were initial reports of several casualties.
Syrian President Ahmed al-Sharaa was attending the opening of a business expo nearly 15 kilometers (9 miles) from the targeted area, one of the Syrian sources added.