Spain, who topped Group B, will now face Italy in the semi finals after two goals from Barcelona full-back Jordi Alba and one Chelsea's Fernando Torres.
The scoreline was cruel on Stephen Keshi's young Super Eagles side, which played some nice football and caused some problems for Spain's defence with John Mikel Obi and Sunday Mba going close.
"We played against a better side, a team who've been together for a long time," Keshi said. "It's a learning process for us, it's good. We have to continue from where we stopped here and build on that."
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