"This was a very difficult game for us," Japan manager Koji Yamamoto said. "Brazil put up a very good fight. But we got some timely hits in the eighth and were able to make a comeback."
Brazil, managed by Hall of Famer Barry Larkin, looked ready to pull off an upset when the tournament debutantes took a 3-2 lead in the fifth inning on a double by Leonardo Reginatto that scored Paulo Orlando from second.
"These players love to compete," Larkin said. "They love a challenge and this was a challenge similar to the qualifiers when we beat Panama. I'm extremely proud of the way my players performed in this game."
Japan is in Group A, which includes 2006 runner-up Cuba and China. Two teams from the group will advance to the March 8-12 second round at Tokyo Dome with a chance to move on to the March 17-19 championship round in San Francisco.
In the other game of the day, Andruw Jones got two hits and Diegomar Markwell and Orlando Yntema combined for seven innings of four-hit ball to help the Netherlands upset South Korea 5-0.
Roger Bernadina drove in two runs and Dutch shortstop Andrelton Simmons went 3-for-5, including two doubles.
Host Taiwan beat Australia 4-1 in the other Group B game earlier Saturday. The Netherlands and Taiwan face off Sunday.