Despite the withdrawal, Seoul plans to send up to 30 people, including five soldiers, to Afghanistan in January to run a hospital that had been managed by South Korean troops at the US military base in Bagram, north of Kabul.
Separately, South Korea has said it is preparing to pull out about 350 troops from Iraq, out of nearly 1,000 it has deployed there, at the beginning of next week.
Roh Moo-hyun, the South Korean president, has said recently he intends to extend the Iraq deployment to boost his country's alliance with the US, but the deployment had been widely criticised.
An extension to the mission is subject to parliamentary approval.
A military official said that a plan to submit a motion to the legislature to extend the deployment was in the works, but was unclear whether lawmakers would endorse it.