Ao Tanaka claimed Japan's second goal after the Video Assistant Referee ruled the ball had not gone out of play before substitute Kaoru Mitoma crossed from the byeline, even though on first viewing it appeared to have done so.
It proved the decisive moment in a stunning performance against a Spain side who were fortunate to join Japan in the knockout stage.
In a tournament that has been full of shocks, this was perhaps the most dramatic night so far, with Spain left relying on the result of Germany's game with Costa Rica for them to progress.
All four teams had started the evening with a chance of progressing but with Spain needing only a draw to qualify, they were not expected to need any favours from elsewhere.
La Roja were cruising at the break after Alvaro Morata headed home Cesar Azpilicueta's cross from close range, but Japan would quickly turn the game - and the whole of Group E - on its head.
The Samurai Blue sent on substitutes Ritsu Doan and Mitoma at half-time and within six minutes of the restart they had both made a huge impact.
Doan equalised with a fierce shot from the edge of the area and, only 142 seconds later, Mitomo retrieved Doan's low cross and found Tanaka to bundle home from close range in dramatic circumstances.
The goal was initially ruled out by the assistant referee who signalled Doan's cross had gone out of play, but the VAR ruled Mitomo had reached it in time.
To the naked eye it appeared over the line, but the decision was made that the curvature of the ball was hanging over the chalk, to the delight of Japan's players.
Things got even worse for Spain when Costa Rica took a surprise lead over Germany moments later, because at that stage they were heading out.
The big screens at Khalifa International Stadium showed the updated group table, to the disbelief of the Spain supporters, and pretty much everyone else here too.
Luis Enrique's side were in big trouble, and were showing few signs of knowing how to rescue themselves, with only Germany's late rally sending La Roja through as group runners-up on goal difference.
Japan's reward for a remarkable performance is a tie with Croatia in the last 16, while a relieved Spain side will face Morocco.
This stadium was the setting for Japan's stunning victory over Germany in their opening game at this tournament, and it clearly inspired them again.
The high-pressing style that undid Germany had unsettled Spain at times in the first half but there were still few signs of what was to come.
Morata appeared set to be the story of the night when he netted his third goal of this tournament, equalling Telmo Zarra's record from 1950 for scoring on his first three World Cup appearances for Spain.
Japan had other ideas, and tore into Spain from the start of the second half, again refusing to let them settle on the ball as they attempted to build from the back.
Doan started their revival, collecting the ball on the edge of the area after another loose pass forward by Simon, and firing in a thunderous shot that Simon got two hands to but could not keep out.
That sent Japan's followers wild but more excitement would quickly follow thanks to Tanaka, albeit after a lengthy VAR check.
Spain still had virtually the whole of the second half to stage a recovery, but they lacked either energy or ideas - or both - and rarely threatened Shuichi Gonda in the Japan goal.
It was only the news of Germany's comeback that allowed the Spain fans to relax in the closing minutes, with the goals that La Roja scored in their opening 7-0 win over Costa Rica proving decisive in sending them through.
-- Courtesy of BBC Sport