Japan were looking to match the achievement of their women's side, who reached their final yesterday with a victory over France by the same scoreline.
They made a great start to the contest, as Yuki Otsu fired them into a 12th-minute lead with a half-volley.
Wantaway Tottenham Hotspur attacker Giovani dos Santos tried to inspire a Mexico comeback, but his curling effort bent inches wide of the post.
The Spurs winger was the provider when Mexico did equalise, as Marco Fabian converted his corner at the near post on the half-hour mark.
Dos Santos very nearly completed the turnaround before the break, but again was narrowly off target with his chipped effort.
With Dos Santos substituted at half-time with a muscular strain, it was left to strike partner Oribe Peralta to be the Mexico hero.
He put his nation in front midway through the second period with a strike from the edge of the box and despite Japanese pressure, Mexico would never surrender their advantage.