Frenkie De Jong's short proximity finish opened the scoring, however Barca were sticking on after Samuel Chukwueze's very much taken leveler in the 76th moment.
Yet, Memphis Depay jumped after the Villarreal guard neglected to clear a long freedom in the 88th moment.
Substitute Philippe Coutinho opened a physical issue time punishment to ensure the outcome and add insult to the injury.
Barcelona stay seventh in the Spanish first class notwithstanding their first away association win of the period, however are currently just three focuses from the Heroes Association spots and seven off pioneers Genuine Madrid.
The success additionally proceeds with new chief Xavi's unbeaten beginning to his term at the Nou Camp, yet there was a lot in the presentation to provide the previous Spain midfielder opportunity to stop and think for thought.
Villarreal every now and again looked like invading his side in the second half with the Arnaut Danjuma and Manu Trigueros speed and development making a grasp of possibilities.
The hosts, who additionally saw a solid first-half case for a punishment dismissed, were left regretting their own cautious weakness through as Colombian Pervis Estupinan permitted Depay in to adjust the attendant and set his side back in front contrary to the rules.
Previous Tottenham safeguard Juan Foyth was to blame for the last objective, stumbling Coutinho in the container to part with an unmistakable punishment.
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