Japan ended Mexico's 100 per cent record with a 3-1 victory at the World Baseball Softball Confederation Premier12.
The host nation battled back from their 3-2 defeat to United States at the Tokyo Dome and have gone joint top of the super round table.
In the day's other match, the US were stunned as they fell to a 2-1 defeat against Australia.
Six teams are contesting the super round, with the top two progressing to the Premier12 final, while third and fourth place will collide.
The top side from the Americas and the top side from Asia who is not Japan will also qualify for the Tokyo 2020 Olympic Games.
Today's results leave Japan and Mexico joint top of the standings with three victories and one defeat each, with the Mexicans closing in on the Americas Olympic spot.
Defending champions South Korea are third with a record of two wins and one loss, while Chinese Taipei are fourth on one win and two defeats.
Australia and the US now both have one win and three defeats and neither can go through to the final.
Every side could still gain one of the Olympic places, however.
Japan scored twice in the opening inning as they triumphed in a game where the pitchers stood out.
The Mexicans only managed one hit, a home run by Jonathan Jones in the fourth inning, as they slipped to their first defeat of the tournament.
Four Japanese pitchers blanked out the rest of the Mexico line-up with 15 strikeouts, as they edged home despite leaving 11 runners on base throughout the match.
Australia's win over the US was historic as it was their first at World Cup or Olympic level.
They scored both of their runs in the first inning and the US could not find a way back.
After a rest day tomorrow, the tournament resumes on Friday (November 15).
The US will play Chinese Taipei with Mexico meeting South Korea.