The soldier, identified only as Im, shot himself in the side and was being sent to hospital, they said.
Sgt. Im’s capture ends a tense stand-off in a forest near his outpost by the border with North Korea.
On Saturday evening Sergeant Im shot and threw a grenade at fellow soldiers before fleeing with his rifle.
Seven others were injured in the attack but are expected to live. It is not clear what was the motive behind his attack.
The incident sparked a massive manhunt, with thousands of troops deployed to block possible escape routes, guard the border between North Korea and South Korea, and protect areas where civilians live, officials said.
Sgt. Im at one point exchanged fire with troops. One soldier was injured, reportedly from friendly fire.
He was eventually cornered on Sunday in a forest in the eastern Gangwon province. His family was brought to the area to persuade him to turn himself in.
Yonhap news agency quoted an army officer as saying that Sgt. Im was in tears as he spoke to his father and brother.
Troops were reportedly so close to Sgt. Im that they could toss him a mobile phone as well as food supplies.
Yonhap earlier quoted an official as saying Sgt. Im had “difficulties” adapting to military life. He was due to be discharged in three months.
There have been similar incidents in South Korea’s military, which operates a conscription system under which all men must serve two years. Bullying and mental health problems have been blamed for previous attacks.
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