"In this case, our opponent was really superior, both in pitching and hitting," said Yamamoto, through an translator. "So we were cornered, in a sense."
Japan had won the first two WBC titles in 2006 and 2009 and were gunning for a third before the Puerto Rican giant-killers worked their magic.
Japanese hitting greats Sadaharu Oh and Tatsunori Hara, who each managed one of the two WBC title teams, threw out the ceremonial first pitches before the game, but the defenders failed to deliver with their bats.
They made outs in their first 10 at-bats against Puerto Rican starter and winner Mario Santiago and then left runners in scoring position in the fourth, fifth and sixth innings.
Perhaps feeling the urgency to make something happen, Yamamoto gambled on calling a double steal with men on first and second and slugger Shinnosuke Abe at the plate after Japan scored their only run with one out in eighth.
The play backfired, however, when lead runner Hirokazu Ibata hesitated after taking a few initial steps toward third. Seiichi Uchikawa put his head down and sprinted for second only to find Ibata standing on the bag.
Puerto Rican catcher Yadier Molina ran all the way out toward second base and tagged Uchikawa out. Abe grounded out harmlessly to end the threat.
Yamamoto said Puerto Rican reliever J.C. Romero's delivery was slow to the plate, making the gamble worth taking.
"It failed, but I don't regret the attempt," he said after joining Venezuela and the U.S. team on Puerto Rico's upset list.
The Japanese manager praised his own players.
"I think (Kenta) Maeda did great pitching," he said about his starter, who gave up just one run in five innings. "I think that the players did great.
"All of them worked really hard and on such a big stage. This is going to be a benefit for their careers as a baseball player in the future."
Unlike the previous two WBC tournaments when Japan featured Major League Baseball players such as Ichiro Suzuki and Daisuke Matsuzaka, the present team did not have a single active major leaguer on their roster.
"We were all domestic players from Nippon baseball," he said. "Despite the challenges they really had the unity to fight for the game."
Yamamoto admitted he felt pressure to live up to Japan's track record.
"Of course I aimed for three consecutive winning championships," he said. "And I had some expectation that we would be able to do that.
"However, this was a great experience."