The six teams that advanced from the First Round to the Super Round were Australia, Chinese Taipei, Japan, Mexico, South Korea, and the United States. Japan defeated South Korea in the championship game, and the bronze medal game was won by Mexico over Team USA.
The top two teams from each group then advanced to the six-team Super Round, which was hosted at ZOZO Marine Stadium and the Tokyo Dome in Japan.
In the Super Round, the top two teams that advanced from each of the three groups competed in a round robin format against the top two teams that advanced from the other two groups, for a total of four games played per team.
Following the conclusion of the Super Round, four teams advanced to the Finals. The four teams were selected based on a combination of the results of the Opening Round game contested between the two teams in the same group that qualified for the Super Round (1 game), plus the teams' results in the Super Round (4 games).
The 3rd- and 4th-place teams competed in a Bronze Medal Game, while the 1st- and 2nd-place teams faced each other in the Championship Final at the Tokyo Dome.
The super-round game between South Korea and the United States played on November 11, which South Korea won 5–1, became a topic of debate due to an alleged misjudgment by an umpire, Tetsuya Shibata, against South Korea in the third inning. Baserunner Kim Ha-seong slid back to home plate before catcher Eric Kratz in the eyes of some was able to tag him out, but Tetsuya ruled it as an out instead. Team Korea's coach, Kim Kyung-moon immediately requested a VAR check, but was refused. Slowed-down television footage was available online, and some criticized the call claiming it was wrong and that South Korea lost a run due to the call. The Korea Baseball Organization held a meeting after the match with the tournament's technical directors and filed an appeal, additionally stating that Kratz physically obstructed Kim's path to home plate in violation of WBSC playing regulations. WBSC responded by saying that they respected Team Korea's perspective and would seek to make improvements in the future. The Japanese media initially kept this incident quiet on the news, and many ridiculed the controversy in Japan.