Neymar had missed a penalty in Barca's 3-1 first leg win three weeks ago, but made amends after just three minutes when he turned home Lionel Messi's cross yesterday.
Jonathan dos Santos gave the hosts hope with an equaliser on the night against his old club, but Villarreal's chances of a famous comeback faded when Tomas Pina was shown a straight red card for a heavy challenge on Neymar.
Luis Suarez slotted home his 11th goal of the season to make it 2-1 before Neymar rounded off the scoring from Xavi's cross late on.
"I am very happy to be in the final again and we have to congratulate the team," said Neymar.
"Villarreal are a great team with a lot of high-quality players. We knew it was going to be a difficult game and that is why we started so well. We scored very quickly and that helped us."
However, victory also came at a cost for Barca as Sergio Busquets was stretchered off in the first-half with a high ankle sprain that could keep him sidelined for a significant couple of weeks with the Catalans set to face Real Madrid in La Liga on March 22.
"It is the bad news of the night without a shadow of a doubt," said Barca boss Luis Enrique.
"I can't give a diagnosis before the doctors look at him. We know he will be out for a while, how long the doctors will decide."
Enrique started Javier Mascherano and Suarez despite both being one yellow card away from missing the final and that decision was vindicated inside three minutes as both were involved in the move that let to Neymar's opener.
The ball eventually found its way to Messi and his tantalising in-swinging cross was looped over Sergio Asenjo by the Brazilian captain.

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