The young El Tri side is set to defend their gold medal triumph in this summer's 2016 Rio Olympics.
Only a minute into the game, Shoya Nakayima's deflected shot beat Gibran Lajud to put the Asian champions in front.
Shortly past the half-hour mark, Japan doubled their lead when a backheel play from Yuya Kubo finished with Takumi Minamino firing home Japan's second.
After going into the break with a two-goal lead, Japan were content to allow Mexico possession and lock down their defense.
Japan's strategy was working just fine until the 68th minute. Marco Bueno struck the ball off a defender but he made up for it by picking up the rebound and sending a deflected volley into the back of the net.
In the closing stages of the game, Japan goalkeeper Kosuke Nakamura sealed the win when he got his finger tips on the ball to divert a Daniel "Fideo" Alvarez shot wide.
Mexico next will play hosts Portugal on Monday in their last game of this European trip.
You can watch highlights of Mexico's defeat below: