With both sides knowing a win would see them advance, Spain wasted little time in hitting the front as Alvaro Morata headed beyond Shuichi Gonda for his third goal of the tournament early on, Trend reports citing Bein Sports.
However, Spain failed to capitalise on their huge dominance of possession as Japan turned the game on its head with a quickfire second-half double, Doan firing home from range before Tanaka bundled in a second.
Spain was briefly on its way out of the World Cup when Costa Rica took the lead against Germany in the group's other fixture.
But Germany's late comeback in a 4-2 win ensured La Roja survived an incredible finale to go through as runners-up.