Maming Bin Mama, 21 and Sagrueara Jaehsea, 25, confessed on yesterday to gunning down the brothers -- aged three, five and nine -- as they returned home from a local mosque in Bacho at the start of February.
The men also shot the boys' mother, who was pregnant, although she survived the attack.
The district is among the most volatile in Narathiwat province -- one of three Muslim-majority southern provinces blighted by a decade-long insurgency which has claimed around 6,000 lives.
The father was arrested but later released with insufficient evidence to prosecute him.
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"They (the rangers) confessed that the killings were motivated by revenge," provincial police commander Pattanawuth Angkanawin told AFP, adding the men gunned down the children by accident as they tried to kill the father -- who escaped unharmed.
Another suspect was still at large, Pattanawuth added. The two men remain in custody.
Rebels blamed Thai authorities for the boys' murder and several Buddhists were killed over the following days in apparent revenge, including two women, a monk and a nine-year-old boy.
Shadowy insurgents are fighting for a level of autonomy for the south from Buddhist-majority Thailand, which annexed the region more than one hundred years ago.
The roots of the insurgency draw on long-standing anger at efforts by Thailand to assimilate ethnic Malay Muslims and at a perceived lack of respect for local language, religion and customs.
The majority of the dead have been civilians, caught between warring rebels and Thai security forces, who rights groups accuse of acting with impunity.