The friendly match was to prepare for next week’s important 2010 World Cup qualifier against UAE for South Korea and Japan for Uzbekistan.
Ki volleyed home from the edge of the area in the third minute for his second goal in three internationals.
Substitute Lee curled the ball into the top corner in the 83rd minute and added another with four minutes left.
It was the first match for Uzbekistan coach Mirdjalal Kasimov. The former midfielder took the job last month.
So far in the final round of Asian qualification, South Korea has one point from one match in Group Two. Uzbekistan has two straight defeats in Group One and takes on Japan on Wednesday. The top two teams from each of the two groups of five automatically qualify for the 2010 World Cup.