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In a repeat of the tournament's first final in 2006, Alfredo Despaigne fired a three-run homer for a 6-0 lead and it proved critical as Japan clawed back to 6-3 before finally succumbing to their first defeat to Cuba in the global event.
With Cuba and Japan already through from Pool A, the game's main significance was to provide pointers for round two, and both teams will claim to have gained a psychological boost as the round-robin phase concluded in Fukuoka.
Cuba will play Pool B runners-up the Netherlands when the second round gets underway in Tokyo on Friday, while Japan will take on fellow co-hosts Taiwan. The top two teams will advance to the final round later this month in San Francisco.
After the first six batters were shut out by Japanese starter Kenji Otonari in the first two innings, Cuba took a 1-0 lead when Yasmany Tomas hit a solo home run in the bottom of the third inning.
In the fourth inning, Jose Fernandez hit a single and then slugger Frederich Cepeda unleashed a double to get him home and enlarge the lead to 2-0, before ace pitcher Masahiro Tanaka struck out the next three batters.
The Japanese, roared on by a partisan home crowd, had their chances when they took second base three times in the second, third and fourth innings, but they were never able to cash in.
Japan missed another chance in the sixth inning with the first and third bases loaded at one down, only to see Atsunori Inaba ground out for a double play.
Jose Abreu hit a sizzling single to welcome Fernandez from the third and make it 3-0 in the sixth inning, before Despaigne's home run for 6-0 in the eighth.
Japan finally scored in the ninth inning when Hisayoshi Chono hit a single with three bases occupied. Takashi Toritani then hit a sarifice fly for 2-6, and Hirokazu Ibata hit a single to trail 3-6.
But Ryoji Aikawa swung out with two runners still on the first and second bases as the miracle comeback petered out.
It was Cuba's first win over Japan in four games in the tournament, including their 6-10 defeat in the inaugural final in 2006.