Scotland's best chance of the game came with their first attack.
Napoli star Scott McTominay charged into the box to meet John McGinn's cross from the right, but was denied by an excellent save by goalkeeper Zion Suzuki, who managed to turn the shot on to the post.
Despite that bright Scotland start, it was the visitors who slowly but surely took control.
Kodai Sano shot straight at Gunn from long range and then fired too high, Yuito Suzuki could not beat the goalkeeper after driving into the box, and Ao Tanaka's first-time shot flicked the bar on its way over.
Scotland improved after half-time, forcing Japan to go long and creating chances of their own without applying the crucial final touch.
McTominay had a looping header clear the bar before forcing Suzuki into a save from a free-kick, while captain Andy Robertson stung the goalkeeper's palms following a powerful driving run.
Being a friendly, both teams made numerous changes, and as in the first half, Japan seized command as the half progressed.
Brighton's Kaoro Mitoma - off the bench for the visitors - could not hit the target after a corner broke to him on the edge of the box and fellow substitute Ito had a shot smothered by Gunn after skipping past Jack Hendry.
Ipswich striker George Hirst rippled the side-netting after replacing Lyndon Dykes, but it was Ito who popped up at the other end to settle the contest.
Hajime Moriyasu's side have lost just five of their past 40 matches since the 2022 World Cup in Qatar, while Scotland have not won a home friendly since March 2016 when they beat Denmark.
More to follow.