Israel finished third in the quarter-final group, ahead of Cuba, but behind Japan and the Netherlands who advance to next week's semi-finals in Los Angeles.
True to form Team Israel were plucky and impressive against the world's top-ranked team in the Tokyo Dome. Tight pitching by both sides saw the game deadlocked for nearly two hours with Israeli pitcher Josh Zeid, excellent throughout the tournament, keeping the Japanese big hitters at bay.
The sixth innings was the undoing of Israel as substitute pitcher Dylan Axelrod was hit all over the park as the Japanese raced to a 5-0 lead.
More runs in the eighth and ninth innings gave the home team an unassailable 8-0 lead.
But Israel ended the tournament with a flourish with star batsmen Ryan Lavarnway, Zach Borenstein and Ty Kelly scoring consolation runs.
Israel may be going home (or rather back to the US as all the players are US Jews and only three have Israeli citizenship) but after a series of four fairytale victories over teams ranked in the world's top 10- Korea, Taipei, the Netherlands (in the final 16 group stage) and Cuba in the first of three matches in the round robin last eight group, Israel ranked 41 can take much pride from its first ever World Baseball Classic appearance.
Israel now automatically qualifies for the 2021 World Baseball Classic by virtue of reaching the last eight.