Yuya Osako scored twice in the second half after Manabu Saito opened the account in the first half for Japan, who earned their first win of the tournament at Hwaseong Stadium, south of Seoul.
Osako, in his first international match, broke a 2-2 deadlock with his second goal of the game in the 79th minute, hardly a minute after the Socceroos pulled even on Tomi Juric's goal.
Alberto Zaccheroni completely overhauled his Japanese starting line-up from last Sunday's 3-3 draw against China PR. For Australia, Holger Osieck trotted out the same starting 11 that he used in the scoreless draw against Korea Republic last Saturday.
After a feeling-out period, Saito put Japan ahead in the 25th minute with his first international goal. He took a pass near the arc and dribbled toward the right edge of the box, before chipping one out of Eugene Galekovic's reach into the Australian net.
Japan threatened to go two-up 11 minutes later, but Yohei Toyoda's header off a Hiroki Yamada cross went right into Galekovic.
Australia tried to mount a comeback, as Matthew McKay volleyed a loose ball high over the bar in the 40th minute.
Australia showed more life to start the second half but Japan pulled away in the 55th. Osako received a nifty pass from Toyoda under the arc and dribbled in between two Australia defenders before calmly putting it past Galekovic.
The goal gave the Australians new life, and Juric netted the equaliser thanks to a great individual effort from the top of the box.
Korea DPR controlled the pace for most of the first half, and Ri Ye-Gyong hit the crossbar just before the break. Japan made some last-ditch efforts to beat the fatigued opponents, but Hong Myong-Hui stood her ground in the North Korean net to keep the match scoreless.