Lee scored in the 72nd and 85th minutes, while midfielder Ki Sung-Yueng gave the home side an early lead by netting a volley in the third minute, Yonhap news agency reported.
South Korea face the United Arab Emirates at home on Wednesday in an Asian qualifier for the 2010 FIFA World Cup South Africa™.
South Korea drew with Korea DPR last month in their opener for the final qualifying round. South Korea are grouped with the UAE, Saudi Arabia, Korea DPR and Iran in Asian Group B.
Ten Asian teams are competing in the final qualifying series, with the two top teams from each group of five allowed to advance to the World Cup finals.