The match, originally scheduled to take place in the North Korean capital of Pyongyang, was moved to the Chinese city of Shanghai due to the refusal of the North Korean authorities to allow the South Koreans to fly their flag or play their anthem on the territory of the secretive communist state.
The two countries have yet to sign a formal peace deal following the 1950-53 Korean War.
The game was part of the fourth round of the Asian Football Confederation qualifiers for the 2010 World Cup in South Africa.
The two sides met twice in the third round, with both teams getting out of the group. In March, in a match that was also moved to Shanghai, the teams drew 0-0. In the return fixture in Seoul, during which the South permitted the North to raise its flag and play its anthem, there was again nothing between the teams, and the tie ended 1-1.
In Wednesday's game, the nominal hosts went ahead through a 64th minute penalty converted by Hong Yong Jo before South Korea's Ki Sung Yueng leveled the score five minutes later.
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South Korea are looking to make their seventh consecutive World Cup finals. North Korea have appeared only once at the finals, famously beating Italy 1-0 before losing 5-3 to Portugal, after going 3-0 ahead, in the quarter finals.
