The incident has threatened to increase tension along the Israeli-Lebanese border.
Sayyed Hassan Nasrallah, the leader of Hizb Allah fighters, had vowed retaliation before the body of the 17-year-old was found.
“This Lebanese civilian should be quickly returned to Lebanon,” Nasrallah said on Wednesday when the shepherd was still missing and presumed captured by Israeli forces.
“From now I say that if [it turns out that] this civilian had been killed then the resistance would punish the killers without hesitation or any discussion.”
Hizb Allah fighters have periodically attacked Israeli forces on the border, mainly in the occupied Shebaa Farms, since Israel ended its 22-year occupation of south Lebanon in 2000.
Lebanon says Shebaa is Lebanese. The United Nations and Israel say it is Syrian land. Hizb Allah says its attacks are in retaliation to Israeli infringements on Lebanese sovereignty, including almost daily flights by Israeli warplanes.
The Security Council authorised UN peacekeepers this week to remain another six months in south Lebanon. The force had deployed in the area after an Israeli invasion in 1978.