South Korea had already qualified for South Africa.
Iran are level on points in Asian qualifying Group Two with North Korea and Saudi Arabia, who meet later on Wednesday, and need the Saudis to lose to secure a playoff place.
Several Iran players wore green armbands early in the match in what appeared to be a show of support for defeated presidential candidate Mirhossein Mousavi while their fans unfurled banners at the stadium reading: "Free Iran".
Iran went ahead through an own goal in the 51st minute from South Korea's Kim Dong-jin, who was tightly marking Iran's Masoud Shojaei. Kim was hit by a cross and the ball slid past helpless goalkeeper Lee Woon-jae.
South Korea equalised through a masterful goal from Park Ji-sung. The Manchester United midfielder took a short pass from Lee Keun-ho, beat a defender and tucked a left-foot shot just under the bar in the 81st minute.
Iran, fourth in the standings going into the match, needed to beat group leaders South Korea and hope North Korea and Saudi Arabia drew to secure the second automatic qualification slot.
South Korea will be playing in their seventh consecutive World Cup finals.
