Yusuke Komiyama and Mitsuyoshi Matsumiya scored in the first half for the Group D winners before Tetsuya Murakami and Shota Hoshi sealed a fourth consecutive win after the break.
Japan will face China on day for a place in the final after China earlier surprised Thailand 9-2 to reach the semi-finals courtesy of a hat-trick from midfielder Zhang Xi.
Kyrgyzstan had only scrapped into the last eight as runners-up in Group C with one victory after a 4-4 draw against winless Korea Republic in the final group game on Tuesday secured a place in the quarter-finals after Thailand beat Vietnam.
And coach Amirzhan Mukanov knew Kyrgyzstan faced a tough task against Japan despite Miguel Rodrigo’s side only managing to beat Turkmenistan 1-0 in their final Group D game.
Kyrgyzstan held out for eight minutes before Komiyama opened the scoring, with fellow substitute Matsumiya doubling the advantage four minutes from the interval.
Murakami added a third with seven minutes remaining before substitute Hoshi sealed the win in the last minute.