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Troops cornered the 22-year-old soldier in a densely forested area near a small town in Goseong county, a mountainous region on the eastern coast of the peninsula near the border with North Korea.
After a 24-hour stand-off and despite pleas by his father to give himself up, the conscript shot himself in the side, and was taken to a military hospital.
Late on Saturday night the soldier threw a grenade and opened fire, killing five members of his unit and wounding seven at a base outpost in Goseong county. The conscript then fled carrying a firearm, ammunition and a grenade and exchanged gunfire with troops.
The soldier, identified as Sergeant Lim, was described by an official as an "introvert" and said there had been earlier concerns over his psychological health, but he was deemed fit to be deployed to the outpost after passing a test in November.
The military has been criticised before for lax discipline in some units and failure to prevent previous cases where soldiers, suffering personal problems, have shot fellow soldiers.
In a similar incident in 2011, a South Korean marine went on a shooting spree at a base near the tense maritime border with North Korea, killing four fellow soldiers before trying to blow himself up with a hand grenade.
Defence ministry spokesman Kim Min-seok said a large number of conscript soldiers, most of whom are in their early 20s, are classified as "of interest" and are under supervision by the command for concerns over potential disciplinary or mental health issues.
About 800 soldiers of the 22nd Infantry Division that serves the Goseong region, or 9 percent of division force, are under supervision, Kim said. Lim was one of them.
All able-bodied South Korean men serve about two years under a conscription system that makes up a large part of the 600,000 active service troops, and there are concerns that new recruits are softer and find it harder to adapt to military life.