Eight players and coaches from the Mariners and Athletics went to Ishinomaki on the northeast coast and later put on a baseball clinic for students affected by the catastrophe.
More than 19,000 people in Japan were killed by the disaster on March 11, 2011. About 46 percent of Ishinomaki, a city of 150,000, was inundated by up 32 feet of water.
Much of the city remains in ruins. Destroyed cars are stacked five or six high next to huge piles of wreckage that have yet to be cleared away. Many homes near the shoreline were washed away.
"There is an air of silence you have in the car when you drive through it and see it," Seattle manager Eric Wedge said. "That's just a small stretch. You picture that times 150 miles and its just pure devastation."
Major League Baseball made a donation of $500,000 to the city to help in reconstruction efforts.
After a bus tour of the disaster zone, the players conducted a baseball clinic with students from the area, many of whom had homes destroyed or lost family members.
"Of all the things I had to do here this is the one I wanted to do most," Oakland pitcher Tommy Milone said. "Obviously, we do clinics back home, but to be able to give back to these kids who have lost homes and family members is something special."
Seattle pitcher Hisashi Iwakuma, who played last season in Sendai, the city closest to the disaster zone, got the biggest round of applause when the players were introduced at Ishinomaki Municipal Stadium.
"Meeting Iwakuma was awesome," said 11-year-old pitcher Masayuki Kondo. "He praised my pitching and told me I was doing a good job."
The teams are in Japan to open MLB's 2012 season with games on Wednesday and Thursday at Tokyo Dome.