The victory means Cuba wins Pool A and will begin the second round against The Kingdom of the Netherlands, the Pool B runner-up. Japan, the second-place team in Pool A, opens the next round against Pool B winner Chinese Taipei. The second round begins Friday at Tokyo Dome.
All the games will be televised on MLB Network and ESPN Deportes in the United States, and tickets can be purchased for any of the remaining games at www.worldbaseballclassic.com.
"We are very happy," Mesa said through a translator. "Tonight's win has a lot of meaning. We got a lot of confidence from that."
The Cuban hitters gave their manager a lot to feel good about.
Yasmany Tomas hit a solo home run in the third, and Alfredo Despaigne capped Cuba's night with a three-run shot in the eighth.
Despaigne went 2-for-4 with three RBIs during the game and ended the first round 4-for-8 with a double, a home run and five RBIs in three games. He was named MVP of the pool.
"I'm very satisfied with what I did," Despaigne said through a translator. "It's a wonderful experience."
Cuban second baseman Jose Fernandez was 2-for-3, while Frederich Cepeda went 1-for-3 with an RBI double to wrap up a strong first-round showing with a .500 average (5-for-10), two doubles, a triple and a pair of RBIs.
The victory was Cuba's first over Japan in Classic competition. The Japanese beat the Cubans in the 2006 final and twice during the second round in 2009.
"Japan is a very solid team," Despaigne said. "They are a really nice team. Also, they are the two-time defending champions. It's always tough to play against Japan."
The Japanese struggled at the plate for the third straight game and were a dismal 2-for-9 with runners in scoring position. Japan was limited to seven singles and left 10 men on base.
"Some of the hitters are in good condition, but some aren't," Japan manager Koji Yamamoto said.
Something Japan will be able to take from the game is that struggling ace Masahiro Tanaka looked good in a relief appearance.
Tanaka entered in the fourth, and it looked like his slow start to the Classic would continue when he immediately gave up a single to Fernandez and Cepeda's RBI double. Tanaka struck out the next batter, Jose Abreu, then gave up a single to Despaigne.
Then Tanaka clicked, and the right-hander began to effectively utilize his well-stocked arsenal of breaking balls. Tanaka struck out the next two batters to end the fourth and fanned the side in the fifth.
Overall, Tanaka pitched two innings, allowing one run on three hits and striking out six.
"Today's result wasn't so bad," Yamamoto said of Tanaka's outing. "So he can be used as a reliever, or he can be used as a starter.
Cuban starter Wilber Perez was the winning pitcher, striking out three over three scoreless innings.
Pitching at home wasn't enough for the Fukuoka Softbank Hawks' (Nippon Professional Baseball) Kenji Otonari, who was saddled with the loss after allowing a run on two hits in three innings.
Tomas crushed one of Otonari's sliders and sent it deep into the left-field seats to put the Cubans ahead, 1-0, in the third.
Cepeda doubled in a run in the fourth, and Fernandez gave reliever Hirokazu Sawamura the same treatment he gave Tanaka with a double to start the bottom of the sixth. Fernandez moved to third on a Cepeda groundout and Abreu drove him in with a single.
Cepeda drew a one-out walk in the eighth, and Abreu singled to put two on for Cuba. Despaigne cleared the bases with a home run deep to left-center.
The Cuban bullpen then nearly coughed up the lead in the ninth.
Sho Nakata and pinch-hitters Katsuya Kaunaka and Yuichi Honda all drew one-out walks to load the bases for Japan.
Hisayoshi Chono drove in one run with a single and Takashi Toritani plated another with a sacrifice fly. Hirokazu Ibata added an RBI single to make the score 6-3 before Ryoji Aikawa struck out to end the game.