Participating in the game at Tokyo Dome on Sunday will be a group of student baseball players from the Tohoku region that was devastated by the 2011 disaster that killed over 15,000 people. Profits will go toward helping children in the region.
Jeter and Matsui will also put on a baseball clinic and take part in a home run derby.
Jeter, who retired from Major League Baseball last year after 20 years, said he's looking forward to a break from the game.
"I need to get away from (baseball) for a little while, I've been doing it professionally for 23 years," Jeter said at a news conference. "At this moment, I'm not thinking about getting back in the game. My ultimate dream is to one day own a team, but that's in the future."
Recalling his own experiences after the Sept. 11, 2001, terrorist attacks in New York, Jeter said he was hoping to help children in Japan who are still dealing with the aftermath of the disaster. While the earthquake and tsunami struck four years ago, many of the participants from the area are still coping with the loss of family and friends and living in temporary housing.
"The kids will never forget what happened," Jeter said. "But if they can come out and have fun and enjoy themselves through the sport of baseball, that's what we're trying to do here."
Matsui, the 2009 World Series Most Valuable Player, said Jeter's presence will go a long way.
"Having Jeter here is a wonderful thing," Matsui said. "I'm happy, and the kids taking part in this event will be thrilled. We hope they have a great time, and return to Tohoku with some great memories."
Matsui was recently rehired by the New York Yankees as a special adviser to general manager Brian Cashman, and Jeter said his former teammate will have much to offer.
"Not only was he successful here in Japan, one of the biggest stars in the country, he came over the United States and did the exact same thing," Jeter said. "There aren't too many players that can say that ... so he has a lot of knowledge, and will be able to share that with as many people as he wants to do."