Both sides carved out chances early on at Hampden Park with Scott McTominay denied by a spectacular Zion Suzuki save after just eight minutes.
John McGinn’s graft down Scotland’s right side created the opportunity for the Napoli star on the six-yard line, but Suzuki’s razor-sharp reactions tipped his prodded effort onto the post.
Japan’s threat was largely contained to pot shots from distance in the opening half-hour - with Daizen Maeda and Kodai Sano both repelled - before Leeds United’s Ao Tanaka clipped Angus Gunn’s crossbar from 15 yards on 38 minutes.
Japan made a flurry of changes at HT to try and force a breakthrough with Brighton & Hove Albion winger Kaoru Mitoma introduced by Hajime Moriyasu and the Seagulls star was inches away from teeing up Keisuke Goto on 53 minutes.
That triggered a quickfire response from Scotland, as a sprawling Suzuki stop thwarted captain Andy Robertson less than a minute later, and the contest flowed from end-to-end.
Mitoma continued to pull the strings for Japan, as his cute through ball created another chance - this time wasted by fellow sub Ito - before Japan’s No.7 saw a goal-bound effort cleared off the line by McLean on 68 minutes.
Scotland looked to hang on in the closing stages, but their defensive resilience was eventually punctured with six minutes to play, as Mitoma crisply released the overlapping Junnosuke Suzuki and his low cross was poked home from close range by the redeemed Ito.
Defeat on home soil ends Steve Clarke’s unbeaten Hampden streak at three games with Japan also stopping his team from scoring for the first time in their last six outings.
Next up for the Tartan Army is a clash with the Ivory Coast at Everton’s Hill Dickinson Stadium on March 31 as Japan take on England at Wembley.
Flashscore Man of the Match: Kaoru Mitoma (Japan)