The soldier shot and injured by the North Korean side while defecting from a military post in front of Panmungak, the main building managed by North Korea in the Joint Security Area, the JCS said in a statement.
It was the first shooting in the Joint Security Area since 1984, but USA and South Korean forces did not return fire.
Crossing into South Korea is particularly treacherous as the border is marked by trigger-happy soldiers on both sides.
He was shot in the shoulder and elbow and was taken to a South Korean hospital, the Defence Ministry said.
The Unification Ministry said North Korean soldiers also defected across the JSA in 2007 and 1998, but military officials said no shooting occurred during those incidents.
But there was no direct exchange of gunfire between South and North Korean guards in the process.
The soldier drove a jeep toward a guard post in the Joint Security Area just after 3 p.m. on Monday, said Col. Roh Jae-cheon, a spokesman for South Korea's Joint Chiefs of Staff. We wonder what our military did even when North Korea made a serious provocation again by violating the decades-old cease-fire agreement in the tense border.
The soldier was found near the border village of Panmunjom, about 50 metres south of the Military Demarcation Line. They stand only several yards away from tall South Korean soldiers wearing aviator sunglasses and standing motionless like statues.
The defection came during escalated tensions between the North and the South and almost a week after President Trump visited Seoul for his five-country Asia tour. More than a million mines are believed to be buried inside the zone. South Korean troops didn't fire at the North, he said.
From there they can seek sanctuary and organise a flight to South Korea, where defectors are given assistance and prepared for life outside the hermit state.
The area is a popular place for tourists and visiting officials, not least because once inside the blue meeting huts that straddle the border, visitors can technically cross the line, although soldiers guard the doors out to the other side. That prompted Washington to send nuclear-capable B-52 bombers to intimidate the North before the adversaries pulled back from the brink of conflict.
Areas around Panmunjom were the site of bloodshed and defection attempts by North Koreans in the past, but there have been no such incidents in recent years.