They had been giving chase when they were "ambushed and came under fire," it said.
In an initial statement it said two soldiers had been shot dead, but later reported that a third had succumbed to his wounds.
It said one gunman was also killed and the driver of the vehicle was arrested, without giving further details.
It was a rare attack on the Lebanese army and the circumstances around it remain unclear.
Hermel region is close to the border with Syria.
Lebanon's prime minister Hassan Diab condemned the ambush, saying an attack on the army is an attack on all Lebanese.
"What is required at this moment is to speed up the arrest of the attackers," he said, without identifying those responsible, in a statement carried by state-run National News agency.
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