The bomb exploded in the early afternoon at a car park in a Yala province technical college where an army car was parked, Police said on Monday.
The explosion injured four soldiers, one seriously, as they were about to begin patrolling the area.
"It is possible that the attackers aimed to attack soldiers as the area was a stand-by point for soldiers," said Yala police general Sirichai Thanyasiri.
Airports, railway stations and other tourist destinations in southern Thailand were on full alert after three blasts on Sunday rocked Songkhla province.
"We have to check the security at all airports and railway stations in southern Thailand," Deputy Minister of Transport and Communications Phumtham Wechayachai told reporters on Monday.
Three blasts at the Hat Yai airport on Sunday killed two people and wounded a total of 74 others, including an American woman, a French woman and two people from Brunei, the Public Health Ministry said.
No one claimed responsibility for the blasts.
Violence in Thailand's Muslim-dominated southernmost provinces of Narathiwat, Yala and Pattani, where shootings or small bombings have occurred almost daily since January 2004, has claimed the lives of more than 630 people.