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.
The Israeli military does not comment on air operations, but there were no reports from Jerusalem of any planes being hit.
Israeli warplanes frequently fly over Lebanese airspace in what Israel says are reconnaissance missions, but this was the first time the army has fired on the aircraft since an Aug. 14, 2006 cease-fire ended a month-long war between Israeli and Hezbollah guerrillas.
Earlier this year, Lebanese and Israeli soldiers briefly exchanged fire near the border village of Maroun el-Rass where the U.N.-demarcated Blue Line was not clearly marked. There were no casualties.
Israeli overflights have been a constant source of tension between the two countries. Before last year's war, Hezbollah used to open fire on Israeli planes, with shrapnel from the anti-aircraft fire falling on Israeli communities across the border, causing some casualties.
The deployment of about 15,000 Lebanese troops in the south along with some 13,000 U.N. peacekeepers after the U.N.-brokered ceasefire has not stopped the flyovers despite the U.N. describing them as a violation of Lebanese sovereignty.