The soldiers were returning to their base from patrol on motorcycles in Pattani province when 20 armed militants in three pickup trucks opened fire on the soldiers.
More than 5,000 people have been killed in Buddhist Thailand's three southernmost Muslim dominated provinces of Pattani, Yala and Narathiwat - since an Islamist insurgency erupted in 2004.
Col Pramote Prom-in, a southern army spokesman, said the attackers fled the scene after a brief gun battle.
The incident follows a roadside bomb that killed five policemen in nearby Yala province on Wednesday.
Daily bomb or gun attacks have targeted soldiers and civilians - Buddhists and Muslims, claiming more than 5,000 lives in eight years.
A state of emergency is in force in the worst-affected parts of the region which rights campaigners say gives tens of thousands of military troops based there legal immunity, fuelling rights abuses.
In another incident, an assistant village headman was shot and seriously injured in an ambush in Narathiwat's Rueso district today police said.
Witnesses said told police that gunmen hiding in the roadside forest fired on the assistant headman with M16 assault rifles, before fleeing.
Police has blamed separatist militants.