The latest bombing, in a country destabilised by the civil war in neighboring Syria, was the third such attack in recent weeks in Hermel, a predominantly Shiite Muslim area of Lebanon near the border with Syria.
The bomb was set off when soldiers at the checkpoint became suspicious of the man in the vehicle, a Jeep Grand Cherokee, the sources said.
More than a dozen others were injured of which five are from the army and 10 are civilians.
The explosion happened at Assi Bridge near entrance of Hermel city, Al Jazeera reported.
Jabhat al-Nusra in Lebanon has claimed responsibility for the attack.
Lebanese Prime Minister Tammam Salam said: "The attack on the military establishment exceeds a normal crime. We urge everybody to unite."
It follows a suicide bombing of the Iranian cultural center in Beirut that killed eight people on Wednesday.