The shooting took place early yesterday after Israeli forces identified "suspicious movement" along the border and shot two members of Lebanon's armed forces.
It happened near where a Lebanese army sniper killed an Israeli soldier late on Sunday. There was no information on the condition of the Lebanese soldiers.
The shootings raise the possibility of renewed fighting in the volatile area, which has remained mostly quiet since a month-long summer war in 2006.
The Lebanese army has opened fire in the past after saying Israeli soldiers had tried to infiltrate.
Lieutenant Colonel Peter Lerner, an Israeli army spokesman, said: "We will not tolerate aggression against the state of Israel, and maintain the right to exercise self-defence against perpetrators of attacks against Israel and its civilians."
A UN spokesman said peacekeeping force Unifil was in contact with both the Lebanese and Israeli armies.