The 4-1 result on Saturday evening was Japan's biggest defeat on home soil against the Koreans since 1954 and meant Shin Tae-yong's side retained the regional East Asian Championship title.
Halilhodzic, whose team face Poland, Senegal and Colombia at next year's finals, apologised for the defeat and said he would learn the lessons from the loss.
"I'm sorry to end the year this way, but this is the kind of match that will teach us a lot of things," said Halilhodzic, who led Algeria to the round of 16 in Brazil in 2014.
"We need to look at the current situation for Japan. I know what is waiting for us at the World Cup and this is the kind of match we can learn lessons from.
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"I know a lot and I've absorbed many things so I will work hard so that we do our best at the World Cup."
Few of the squad Halilhodzic selected for the competition are likely to be involved in June, when the Japanese will be making their sixth straight appearance at the finals.
Neither Japan nor South Korea were able to select their Europe-based players due to the timing of the competition.
Halilhodzic was also deprived the services of players from Urawa Red Diamonds due to their involvement in the FIFA Club World Cup.
"I can't compare Japan with Korea, they're incomparable," said Halilhodzic of the team's performance.
"The Japan players did their best, but the World Cup is a different story and I'm not going to bring this squad to the World Cup."
(Reporting by Michael Church in Tokyo, Editing by Sudipto Ganguly)
