Luis Enrique's men had looked distinctly out of sorts at El Madrigal until the teenager's 82nd-minute goal, failing to zip the ball around in their usual manner.
They struggled to get too many sights of Villarreal's goal and only the woodwork meant they were not behind.
Enrique said: "The game was a thrilling one for the public. Both teams took their turns controlling the game and above all shooting at goal. We tried right to the end against a Villarreal that defended very well. The game could have been anybody's. This result is very good for us because it reinforces our playing philosophy."
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