The Socceroos, who drew 0-0 with hosts South Korea in their opening round-robin game, restored parity with two goals in the space of three minutes from Mitchell Duke and Tomi Juric but Osako's winner, immediately after the restart, sealed the result.
Japan coach Alberto Zaccheroni, in his bid to test the bench strength, named a completely different starting 11 from the first match and his young team troubled the Australian defence with their pace from the outset.
After a few close shaves, Australia conceded a goal when Saito deftly placed a right-footed shot past goalkeeper Eugene Galekovic from the edge of the box.
Japan continued to make inroads into the rival defence and were rewarded when Yohei Toyoda's smart flick-on found Osako, who slotted in calmly.
Duke scored his first international goal against the run of play to reduce the margin for Australia while Juric fired home to level the scores immediately after coming off the bench.
The Australians were still celebrating when Osako again finished neatly after a well-crafted move to ensure full points for Japan, who reached the top of the table with four points from two matches.
Hosts South Korea, on two points, will play Japan while China, also on equal points, meet Australia in Sunday's last round of matches.
(Reporting by Sudipto Ganguly in Mumbai; editing by Clare Fallon)
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