In a match were both teams knew victory would secure entry into the knockout stages from Group F, it was the Japanese champions who emerged 1-0 victors at the Edion Stadium.
Neither side was able to find the breakthrough in a tense first half, but Hajime Moriyasu's men claimed second spot in the pool ahead of the Australians thanks to Yamagishi's 72nd-minute goal.
Kang Seung-Jo and Yun Ju-Tae struck either side of half-time to the put the Korean side ahead and, despite Yang Yu's late consolation, those goals proved to be enough.
There was plenty of drama in Group B, as a 94th-minute strike from Sardor Sabirkhodjaev helped Bunyodkor to a 2-1 success at El Jaish and sent Alexander Volkov's men through to the knockout stages ahead of the Qatari club on goals scored.
The visitors moved ahead through a Sergiy Symonenko opener in the 13th minute, but looked to heading for the exit when Mohammed Muntari levelled proceedings shortly after the break.
However, Sabirkhodjaev had the final say with one of the last kicks of the game.
Qualification from Group A had already been claimed by Al Shabab and Al Jazira prior to Wednesday's fixture between the teams - which the former won 2-1 - while Esteghlal gained only pride by beating Al Rayyan 3-1 to finish third.
