The soldier, whose rank and identity have not been disclosed, was flown by helicopter to hospital on Monday after his escape to South Korea in a hail of bullets fired by North Korean soldiers.
Wednesday's surgery was "successful" in terms of staunching bleeding and the soldier had "stabilised much", said Lee Cook-jong, the surgeon in charge of his treatment.
However, he remained unconscious and was not out of the woods, as complications from a severe hip fracture and possible infection remained major concerns, Lee said.
"We will be able to tell you after about 10 days," Lee told reporters at a briefing, when asked about the soldier's chances of surviving.
On Tuesday, government and military officials said the soldier was in critical condition but doctors expected him to live.
The soldier made his escape in a border "peace village" on the heavily guarded demilitarised zone between the two Koreas.
At first, he sped towards the border in a four-wheel drive vehicle but was forced to abandon it and flee on foot when one of its wheels came loose, South Korean officials said earlier.
Doctors removed five bullets from him earlier and one more on Wednesday.
North Korea has remained silent on the issue, while no unusual activity has been detected at the border where the soldier defected, the South's Unification Ministry said.
"There will need to be some questioning on why he defected after his treatment is over," ministry spokesman Baik Tae-hyun told a regular briefing.
Monday was the first time since 2007 a North Korean soldier had defected across the JSA.
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