The Tuesday attack was confirmed by Israeli police and sources in the Lebanese Islamist resistance group itself.
The strike comes in response to an attack by the Israeli airforce just 20km south of the capital on Monday.
Warplanes fired four missiles at a Palestinian resistance base south of Beirut, a Lebanese security source said.
The source said the attack on Monday on Naama village was aimed at an area in which a Damascus-based group, People's Front for the Liberation of Palestine - General Command (PFLP), has a large base.
"There were no casualties as the base had been abandoned some time ago," a Palestinian source said.
In Israel, security officials said the planes raided a "terrorist target" just outside Beirut.
The Israeli sources said the targeted site was used by the PFLP-GC, which is led by Ahmad Jibril.
The air strike was apparently in response to an earlier mortar attack which Israel said targeted one of its naval vessels patrolling in Israeli territorial waters.
The Shebaa Farms is a stretch of Lebanese land captured by Israel in the 1967 Six Day War. Israel did not withdraw from the area when its forces were forced out of South Lebanon in 2001 by a guerrilla war waged by Hizb Allah.