Staff Sergeant Sunil Ratnayake was given capital punishment by a two-judge High Court here while four of the soldier's colleagues were acquitted due to lack of direct evidence against them.
The massacre at the village of Mirusuvil in the Jaffna peninsula came to light when another man in the group of civilians escaped the military attack and raised the alarm.
The incident had occurred on December 19, 2000.
They had gone to check the ruins of their bombed homes following a ferocious bout of fighting between Tal Tiger guerrillas and troops in that area.
Instead of the usual sweeping such allegations under the carpet, the then government of President Chandrika Kumaratunga suspended the entire unit of soldiers and subsequently arrested five men who were indicted in 2003.
Following the lengthy legal process, the final decision was delivered today in a rare case of military being held to account for its actions.
"This is a good example to show the system is working well," Brigadier Jayaweera told reporters.
Sri Lanka's army faces allegations that it killed at least 40,000 Tamil civilians in the final months of fighting that ended in May 2009.
The previous government of strongman Mahinda Rajapaksa maintained that not a single civilian was killed by troops, while his successor Maithruipala Sirisena has agreed to probe the allegations.
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