Chavait Chairuek, an assistant provincial governor, was also killed in the attack and the driver of their car was injured, investigators said.
The car hit a bomb planted on a road in the Bannang Sata district of Yala, the Bangkok Post reported.
National Security Council chief Paradorn Pattanatabut said militant insurgents were responsible for the attack, which he said was meant to put an end to peace talks between the Thai government and opposition leaders.
"Radical militants are flexing their muscles to oppose the peace plan," Paradorn said.
Paradorn said government officials will likely be targeted in future attacks.
"Officials are their target. It's not only security authorities. It includes government officials," he said.