The shootings took place in the village of Ghajar on Tuesday. It is one of the most serious incidents along the border for some months.
A Lebanese police source in Beirut told reporters that several shots were fired at around 17:15 (15:15 GMT) - but he could not give the names of the victims.
Neither the United Nations Interim Forces in Lebanon nor a spokesman for the Shia resistance group Hizb Allah were prepared to comment on the incident.
Ghajar, at the bottom of Mount Hermon, straddles the Israeli-Lebanese border and is inhabited mainly by Alawites, most of whom have obtained Israeli citizenship even though they consider themselves Syrian.
The village is an extension of Syria's Golan Heights, which Israel occupied during the 1967 Arab-Israeli war and then annexed in 1981.
It was not immediately clear exactly where the two men crossed the border.
The Israeli army built a fence two years ago around the part of the village it occupies to prevent infiltrations by villagers and would be Hizb Allah guerrillas.
But sporadic cross-border clashes constantly spark fears of a "new front" opening in the conflict-torn region.
Israel rejected an offer by Syrian President Bashar al-Asad last week to resume peace talks after more than three years.