The contest ended on just one pitch by reliever David Cortes in the top of the ninth inning when Vernon Wells grounded into a game-ending double play with the potential game-tying run on first base.
Jorge Cantu drove in both runs for Mexico of U.S. starter Roger Clemens. Edgar Gonzalez, who threw one inning in relief, was the winning pitcher. Mexico's win put Japan into Saturday's semifinals against Korea, which is unbeaten in the tournament.
The other semifinal pits the Dominican Republic against Cuba. Both games will be played at Petco Park in San Diego.