The Jeonbuk Motors manager replaces Cho Kwang-rae, who was sacked earlier this month in the wake of a 2-1 defeat in Lebanon.
Choi will be charged with leading the team to qualification for the 2014 World Cup.
He was the Korea Football Association's first choice for the role, although he initially rejected the offer, which came just days after he led Jeonbuk to a second K-league title.
Hwangbo Kwan, the chairman of the KFA's technical committee which oversees the national team, claimed Choi was the best choice.
"Through winning the K-League and the Asian Champions League, he has shown his ability in getting the best out of his players," Hwangbo told a press conference in Seoul today.
Earlier in the week, Hwangbo told Korean media it was likely an overseas coach would be appointed. The likes of Guus Hiddink, Sven Goran Eriksson and former Sunderland boss Steve Bruce were linked with the vacancy.
Choi's first game is charged is scheduled to be a vital World Cup qualifier against Kuwait in Seoul on February 29.
The hosts need a point to be sure of a place in the final round of qualification for the tournament.
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