Replays definitely show that plate ump Bob Davidson made the wrong call on Japan's Nishioka leaving 3B too soon. The rule is that a runner can tag and advance as soon as the fielder comes in contact with the fly ball, not catches it.
So Japan did get robbed of a run and an out in the 8th, but they didn't lost the game because of that one call. They lost the game when they didn't manage to plate anyone in the top of the 9th. And the play that really broke their backs was Fujikawa hitting Jeter after the Japanese had thrown out Vernon Wells at 3B on Michael Young's sac bunt attempt.