Colonel Parinya Chaidilok, an army spokesman, said the explosive weighed 30-50 kilogrammes and was hidden in a car with a fake licence plate, which had passed a screening by a bomb detection machine.
Muslims make up more than 90 per cent of the two million people in southern provinces of Yala, Pattani, Narathiwat and Songkhla.
Many complain of being treated as second-class citizens in mainly Buddhist Thailand.
The area was a semi-autonomous Islamic Malay sultanate until annexed by Thailand in 1902.
Several violent uprisings have been put down by the army over the century.
The latest uprising flared in January 2004 when fighters raided an army base, killing four soldiers.
Despite martial law imposed in 2004 and thousands of Thai troops in the region, frequent attacks blamed on Muslim fighters have left around 3,500 people dead.
"The bomb was hidden in the passenger car and detonated by radio signal," he told AFP.
Both incidents occurred in Sungai Kolok, a popular town nearest to the Thai-Malaysia border which has been the target of repeated bombings by separatists in recent years.
Earlier on Tuesday, four gunmen on motorcycles shot and killed a rubber tapper as he travelled to work in Narathiwat province.
That same night in neighbouring Pattani province a home-made bomb injured a police officer and six volunteers at a security checkpoint.
No one has claimed responsibility for the attacks.
On Monday evening a bomb hidden in a motorcycle parked next to a bank was set off during a Buddhist festival in Pattani, injuring 17 people, five of them seriously.
Violence in Thailand's Muslim-majority Yala, Narathiwat and Pattani provinces has claimed more than 3,600 lives since January 2004.
More than 340 people have been killed this year alone.
The Thai government has made little progress towards quelling the unrest despite deploying thousands of paramilitary troops - usually residents hired as armed auxiliaries to the regular military - in the area alongside 30,000 army troops.
The group or groups believed to be behind the attacks have made no public pronouncements but are thought to be fighting for an independent Muslim state.
Tensions have simmered since the region, formerly an autonomous Malay Muslim sultanate, was annexed by predominantly Buddhist Thailand in the early 1900s.
The region's Muslim population have also long complained of discrimination by the central government.