Barca moved a step closer to their fourth Copa showpiece in five years with the home success in the first leg of their semi-final.
Lionel Messi gave the Catalan giants a 41st-minute lead, only for Villarreal's Manuel Trigueros to stun the Camp Nou crowd with a brilliant effort from distance just after the break.
Andres Iniesta and Gerard Pique netted in the second half, though, while Barcelona also missed the chance to score a fourth as Neymar's penalty was saved by Sergio Asenjo.
It was, nevertheless, an impressive win, and one that gives Barca the advantage heading into the second leg at El Madrigal on March 4.
"We have played a very complete game in all phases, against a dangerous team," Luis Enrique is quoted as saying by the club's official Twitter account.
"[It has] not decided the tie and it does not do justice [to us].
"But it is a good result."
Pique added: "We know that [playing at] El Madrigal is very complicated. [But] we are confident."
