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3/18/2013 3:01 A.M. ET

Japan bows out gracefully in first Classic exit

SAN FRANCISCO -- They gathered on the third-base line, their opponents still celebrating wildly on the infield at AT&T Park. In unison, each player on Team Japan removed his cap and bowed toward the field where the jubilant players from Puerto Rico were dancing, a sign of respect in the face of defeat.

With that, the team that had run through the first two editions of the World Baseball Classic with skill and teamwork, using some of their most famous players with Major League credentials to lift them to a pair of championships, had bowed out of the 2013 tournament.

This time, the fundamentals and the team concept simply weren't enough for the Japanese. They didn't have the arms to shut down their opponents when they needed to the most, and their vaunted fundamentals broke down a couple of times in their final game of the tournament -- including a crucial mistake to kill an eighth-inning rally.

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And so it was that, after winning the Classic in 2006 and 2009, Japan found itself eliminated from the 2013 edition Sunday night after a 3-1 loss at the hands of Puerto Rico in the semifinals at AT&T Park. Puerto Rico advances to the Classic final, where it will meet the winner of Monday's semifinal matchup between the undefeated Dominican Republic squad and the upstart club of the Kingdom of the Netherlands.

It was a tough way for Japan to go out after so much success in the tournament over the years, but manager Koji Yamamoto had nothing but kind words for his players after the quest for a third consecutive title had fallen short.

"The players, all of them worked really hard, and on such a big stage of international games, this is going to be a benefit for their career as a baseball player, this season and for the future," Yamamoto said.

The proud tradition of Japanese baseball was honored before the game as all-time great and 2006 Team Japan manager Sadaharu Oh and 2009 manager Tatsunori Hara each threw ceremonial first pitches. After the game, the 2013 manager knew this year's team had not reached its ultimate goal.

"Of course I have aimed for three consecutive winning championships, and I had some expectation that we would be able to do that," Yamamoto said.

Part of the reason was that some of the qualities that took them to the top twice before were missing, with one particular fundamental breakdown in the eighth inning Sunday proving costly.

Down by two with runners on first and second and the go-ahead run at the plate in cleanup hitter and team leader Shinnosuke Abe, a double-steal attempt wound up blowing up for Japan. While Seiichi Uchikawa sprinted from first base, Hirokazu Ibata started and then retreated to second, and catcher Yadier Molina came all the way from behind home plate to tag out Uchikawa about three-quarters of the way up the second-base line.

"There was a sign that the double steal can be attempted, and Ibata's start was a little delayed and that was what happened," Yamamoto said.

As for the call of moving the runners and opening up first base with the cleanup hitter at the plate, Yamamoto said J.C. Romero's motion appeared to be ripe for the picking, so he put on the double steal.

"The motion of the pitching was large, as you can see through the video -- I could see it from the video," Yamamoto said. "And if there's an opportunity, we were saying that the players should run. Slugger Shinnosuke Abe was the hitter and moving forward to the next base is the right attempt. It failed, but I don't regret the attempt."

This year's Japanese team did not feature the Major League star power of its predecessors, with Ichiro Suzuki of the Yankees and Yu Darvish of the Rangers among those who didn't participate in the tournament this time around. The team also previously had Daisuke Matsuzaka earning MVP honors in both 2006 and 2009 while providing clutch pitching performances.

Still, Yamamoto clearly had a lot of pride in the team Japan fielded with all Nippon Professional Baseball League players, the only former Major Leaguer being Kaz Matsui -- who flied out to center for the final out of the game.

"As a team, we were all domestic players from Nippon baseball," Yamamoto said. "It's challenging to get adjusted before the season, so as a team, despite the challenges, they really had the unity to fight the game."

Japan displayed its normal sound defense early in the contest, turning a couple of key double plays to get them out of jams. Third baseman Nobuhiro Matsuda caught a low liner and doubled off a runner to end the second inning, starting pitcher Kenta Maeda started a 1-6-3 double play in the third inning and catcher Abe stopped Jesus Feliciano's attempt to steal to end the top of the fifth.

The team rallied in the late innings and managed to shut down a bases-loaded rally in the top of the ninth to keep their hopes alive. But, this time, it just wasn't enough against a Puerto Rico team that is excelling in all facets of the game.

"In this case, our opponent was really superior, both in pitching and hitting, and so we were cornered, in a sense," Yamamoto said.

John Schlegel is a national reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.