Lebanese security officials said Israel later fired 25 artillery shells into Lebanon.
The military did not immediately report any casualties.
The military said residents of the area have been ordered to remain in their homes.
Today's attack took place near Mount Dov and Shebaa Farms, a disputed tract of land where the borders of Israel, Lebanon and Syria meet.
Lebanese officials said the shelling targeted the border villages of Majidiyeh, Abbasiyeh and Kfar Chouba near the Shebaa Farms area.
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There was no immediate word on casualties.
The attack comes after Israel launched airstrikes today targeting Syrian army artillery posts in response to rockets fired the previous day into the Israeli-held Golan Heights.
The border region has been tense since an airstrike last week in Syria attributed to Israel killed six members of the Lebanese militant group Hezbollah and an Iranian general.
Israel has declined to comment on any connection to the airstrike, but has braced for a response to the strike, beefing up its air defenses and increasing surveillance along its northern frontier.
Lebanon and Syria say Shebaa Farms belong to Lebanon, while the United Nations says the area is part of Syria and that Damascus and Israel should negotiate its fate.