Iran claimed an upset 1-0 win to top Asian qualifying Group A, leaving Korea to claim the runners-up spot on goal difference after an anxious wait on the pitch for news of Uzbekistan's 5-1 triumph over Qatar.
For Korea - perennial qualifiers used to booking a place at World Cups with games to spare - edging through on the final day with a superior goal difference over Uzbekistan of just one was unexpectedly tough.
Choi had talked of booking a passage to Brazil in style by beating Iran and helping the Uzbeks join them in qualifying after accusing Iran of poor hospitality in Tehran last year.
But after another disjointed attacking display, where the Koreans controlled possession but failed to create clear-cut chances, Choi was less bullish in his final assessment.
"It is all my fault," the former Jeonbuk Motors coach said.
"Now that tonight's match turned out this way, I think I need to think over what I need to do from now on."
Choi had arrived as saviour having taken on the role in December 2011 after Korea slumped to a shock 2-1 loss away to Lebanon in an earlier round of qualifiers.
He said he planned to stay in the role only until qualification had been assured and had no interest in leading the side at their ninth finals.
But after big opening fourth-round wins over Lebanon and Qatar, the qualification campaign suffered problems.
A loss away to Iran was followed by a fortunate stoppage-time win over Qatar, while a 96th-minute equaliser was needed in Lebanon this month before Tuesday's defeat.
"Except for the first two games, the performances as well as the results were bad. I feel a lot of responsibility as a coach," Choi told reporters.
"I think being a time-limited coach from the beginning had a negative influence on the team. I hope tonight's defeat becomes a stepping stone for Korean soccer to leap forward."
Angry fans forced the Korea Football Association (KFA) website to shut down due to heavy traffic, while local media jumped in with criticism of Choi, who had led Jeonbuk to the K-League title in 2009 and 2011 with some eye-catching attacking displays.
"What an embarrassing game," South Korean newspaper JoongAng Ilbo posted on its online edition.
"The offense-oriented soccer (which Choi promised) was a mirage."
Korea needed only a draw against Iran to guarantee top spot and qualification for Brazil but Choi said he would "defeat Iran no matter what" so opted to play an attacking lineup on Tuesday.
But they lacked cohesion, and a miserly Iranian defence, which had conceded just two goals in seven previous matches, held out comfortably before they claimed the winner after an hour thanks to forward Reza Ghoochannejhad.
Iran coach Queiroz did not get the apology he demanded from Choi after the "bad manners" comments, but the Portuguese had the last laugh.
He was seen, after the final whistle, smiling with members of the Iranian delegation and with a picture of Choi, photoshopped on to an Uzbekistan shirt, taped to his front.
"We love Korean people and Korean culture. We all know Korean people are kind. But that kind of behaviour is not good," the former Real Madrid manager told reporters.
Queiroz's celebrations, though, drew anger from the KFA, who said he had made a rude gesture after the final whistle that FIFA would be investigating.