Ministers in Seoul also warned their northern neighbours not to repeat what they said was an infraction of the truce.
Footage showed the soldier, named only by his surname, Oh, dash south with at least three troops in pursuit and firing at him.
He was later seen bolting across a road before he collapsed after being hit with at least five bullets. The soldiers withdrew and he was rescued by members of the South Korean armed forces.
Doctors later determined he had been shot in the shoulder, knee and stomach. They also treated him for pre-existing conditions including tuberculosis, hepatitis B, and a case of massive intestinal worms.
The North has not publicly responded to the defection at the sensitive border.
But the incident came at a time of heightened tension between North Korea and the international community over its nuclear weapons program.
South Korean Minister of Defence Song Young-moo issued his warning to the North while on a visit to the border between the two countries.
“Shooting towards the South at a defecting person, that’s a violation of the armistice agreement,” Mr Song said.
The ceasefire accord between North and South was signed at the end of the 1950-53 Korean War.
Mr Song said: “Crossing the military demarcation line, a violation. Carrying automatic rifles (in the JSA), another violation,” he added as he stood near where South Korean soldiers had found Oh, collapsed and bleeding from his wounds.
“North Korea should be informed this sort of thing should never occur again.”
Since the defection, North Korea has reportedly replaced guards stationed there. Soldiers have fortified a section of the area seen aimed at blocking any more defections by digging a trench and planting trees.
Mr Song delivered his rebuke around 10 meters away from the new trees. Four North Korean soldiers were spotted listening closely.
South Korean military officials pointed out two bullet holes in a metal wall on a South Korean building, from North Korean shots fired at Mr Oh as he ran.
Oh has undergone several operations in hospital to remove bullets. His lead surgeon, Lee Cook-jong said his patient has suffers from nightmares about being returned to the North.
Six soldiers, three South Korean and three American, were given awards by the US Forces Korea last week in recognition for their efforts to rescue the defector.
After meeting troops stationed there for lunch, Mr Song praised them for acting "promptly and appropriately".
South Korea has been broadcasting news of the soldier’s defection towards North Korea via loudspeakers, according to the South’s Yonhap news agency, although military officials have declined to confirm that.
Additional reporting by Reuters
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