South Korea reached their eighth consecutive World Cup finals by finishing runners-up in Group A of Asian qualifying but only secured their place on goal difference after losing 1-0 at home to Iran on Tuesday.
Choi took over in December 2011 and said at the time his only mission was to get the team to Brazil and that he would step aside after qualification.
There was little chance of him being asked to reconsider after an unimpressive end to qualifying where the Koreans lost twice to Iran, drew with Lebanon and scored lacklustre wins over Qatar and Uzbekistan.
"The KFA has decided to accept Choi's wish to resign at the end of his contract after having completed the team's qualification for Brazil in 2014," the KFA said.
"We thank him for his efforts and wish him well."
Local media speculated former skipper Hong Myong-bo was in the running to replace Choi as coach.
Hong, who coached the Olympic team to a bronze medal at the London Games last year, captained South Korea to fourth place at the 2002 World Cup under Guus Hiddink.
- Sports & Recreation
- South Korea