There was a silver lining in that they will meet Morocco next rather than 2018 finalists Croatia, but that was little comfort to the Spain coach, who let fly at his players for conceding twice early in the second half.
"I am not happy at all. Yes, we have qualified, I would have liked to be on top of winning this game. This was impossible because in five minutes, Japan scored two goals ... we were out, we were dismantled," Luis Enrique told a news conference after the match.
The 52-year-old coach rejected the idea that he had got his team selection or tactics wrong.
"I didn't miss anything, because we tried it all. We had strikers playing infield, we tried to create the chances. They were defending aggressively, they were closing down the spaces," he said.
"And of course with those aspects, you are going to be in danger ... this is what happens in football, and how can you manage this collapse that we suffered?," he asked with a note of incredulity.
With all four teams still in contention, the group reached a wild climax as the Spaniards took the lead and dominated, only for Japan to come roaring back to ensure Germany's 4-2 win over Costa Rica was not enough to overtake either of them.
Luis Enrique said that he was not aware that Spain were on course to head out of the tournament when Costa Rica led Germany.
"If I had found out, I would have had a heart attack," he said.
