Luis Enrique's side suffered their first defeat of the FIFA World Cup in an unlikely loss to the Japanese.
This is even though La Roja had 83% of possession and put together an astounding 1058 passes throughout.
Spain took the lead in the 11th minute through Alvaro Morata's close-range strike.
However, Hajime Moriyasu's men hit back through Ritsu Doan's 48th-minute long-range finish and Ao Tanaka's controversial 51st-minute effort.
Spain have qualified as runners-up in Group E behind group winners Japan and will face Morocco in the last 16.
Pedri, who played the entire match and made 116 passes, has reacted to the defeat, saying that his side didn't expect to lose (via Barca Blaugranas):
“We knew it was going to be very difficult. Japan put a lot of intensity into it and left very few spaces. It’s a game we didn’t expect to lose."
The Barcelona youngster admitted that Japan's two strikes surprised them:
"The coach told us that they had to take risks. The two goals surprised us... We had to move the ball a lot more and we didn’t."
Spain were heading out of the FIFA World Cup at one stage alongside Germany, who beat Costa Rica 4-2 but did drop out of the tournament.
Pedri touched on when his teammates caught wind of their potential elimination:
“We knew we were out. Personally, I tried to encourage my teammates to look for that goal, but we didn’t manage it. We have to go with everything, the games now are life or death. The coach will tell us the failures we have had and what we have to improve on.”
France's Randal Kolo Muani praises Barcelona's Robert Lewandowski ahead of FIFA World Cup last 16 clash
France have qualified for the last 16 of the FIFA World Cup as winners of Group D and will face Poland on Saturday, 3 December.
Lewandowski's Polish side clinched their place in the Round of 16 dramatically, finishing second in Group C.
Poland finished level on four points with third-placed Mexico but boasted a superior goal difference of one more goal.
Lewandowski scored his first FIFA World Cup tournament goal in Bialo-Czerwoni's 2-0 win over Saudi Arabia.
Muani, who started in Les Bleus' shock 1-0 defeat to Tunisia in their final group stage game, has lauded the Barcelona man as one of the best strikers in the world.
He said (via Barca Universal):
“Robert Lewandowski is an inspiration, he is one of the best strikers in the world and he scores a lot of goals. He is a player who feels comfortable with the ball at his feet despite his great height. I will have to watch him closely.”