At the Jamsil Olympic Stadium in Seoul, Yoichiro Kakitani grabbed a brace for the champions, including the vital clincher in injury time, which gave Japan seven points at the end of the tournament, two ahead of China PR.
Earlier on, China PR had defeated Australia 4-3 but had to wait for the final tournament game to know whether they had won overall. Korea Republic and China have each won two East Asian Cups, while Japan has been the runner-up three times.
The South Koreans, without a goal in their two previous matches, appeared intent on ending the drought from the onset, but they dominated the ball to no avail in the opening 20 minutes.
Japan then surprised Korea Republic with Kakitani's breakaway goal in the 24th. Toshihiro Aoyama delivered a looping pass from his own half to send Kakitani in alone on the South Korean goalkeeper Jung Sungryong and the Cerezo Osaka striker rolled it in to give his side the lead.
Japan's advantage, however, lasted only eight minutes. Yun Illok, after an accomplished give-and-go with Lee Seunggi, struck the ball into the top right corner, out of keeper Shusaku Nishikawa's reach.
The teams engaged in some back-and-forth action in the second half, though neither mounted much pressure until Kakitani finally broke the tie. The 23-year-old forward found himself at the right place at the right time, as he banged home a rebound after Jung made a stop on Genki Haraguchi.
Earlier, China PR struck three second-half goals and held off a last-minute Australian charge for the narrow victory.