The Syrian army responded by firing a surface-to-air missile in the direction of the aircraft, the commander said.
Thursday's report gave no further details.
The Israeli military declined to comment on the reports.
Back in April 2015, Israeli Prime Minister Benjamin Netanyahu officially admitted for the first time that the regime's military had conducted strikes in Syrian territory. Lebanese news site Elnashra reported on Wednesday evening that the attack had hit a location in the periphery of the Syrian city of Homs, an area that had been devastated by the continuing Syrian civil war.
Israel said last month it had attacked Syrian government artillery after fire from across the armistice line hit the Israeli-occupied Golan Heights, and warned it would step up such retaliation in the future.
Israeli officials have expressed deep concern at Iranian influence in Syria, where Iran-backed groups have played a critical role fighting in support of President Bashar al-Assad during the conflict that erupted in 2011.
Hezbollah sees the area south of Homs as within its sphere of interest because it is close to the Lebanese border.
Earlier in the night, residents of eastern Lebanon reported seeing Israeli jets flying overhead.