The drive-by shooting in the Ruso district of Narathiwat province took place shortly before noon on yesterday (July 16), the last day of the holy Muslim month of Ramadan, a period when the region often sees a surge in attacks.
"Around nine gunmen on a pick-up truck followed the victims (in their pick-up truck) and first shot dead the driver," district police chief Rueangsak Buadaeng told AFP, explaining the driver, aged 29, was one of the soldiers killed.
As the vehicle crashed into roadside food stalls, a second soldier, 22, was also shot dead, he said.
Their bodies were then set alight in the truck, Rueangsak added.
Police are still questioning eyewitnesses and have not made any arrests yet.
Rueangsak said three protest banners were found in the Ruso district yesterday with one reading "colonisers are inhumane and always lie to the international community".
Last Friday, four separate bomb blasts in the south left three people dead while a further four people were killed in shooting and arson attacks.
Thailand's junta, which ousted an elected government in a May 2014 coup, has vowed to reboot a stalled peace process with several rebel groups operating in the deep south but so far there has been little progress.
Today Muslims in the southern provinces joined millions around the world in marking Eid, which signifies the end of Ramadan, offering prayers for deceased relatives at cemeteries and donating money to those less well off.