Lebanese soldiers opened up with machine guns and light anti-aircraft weapons mounted on armored vehicles at two planes that flew by just east of Marjayoun town near the border at midmorning, a Lebanese security official said.
A total of 150 rounds were fired, he added. A senior military officer also said the army "confronted" the Israeli planes, but gave no details.
Both officials spoke on condition of anonymity in the absence of a formal announcement from the military command.
Israeli warplanes frequently fly over Lebanese airspace in what Israel says are reconnaissance missions, but this was the first time the army has on the aircraft since an August 14, 2006 cease-fire ended a month-long war between Israeli and Hizbullah guerrillas.
It is also the first time since February that the Lebanese army, which deployed in the south after the fighting, has fired on the Israelis.