The club have confirmed the offender's season ticket has been revoked and affirmed its commitment to fighting racism and discrimination.
The Brazilian picked up and ate the fruit thrown at him from the stands as he prepared to take a corner, before later issuing ironic thanks to the offender after Barca came back from 2-0 down to win 3-2.
Villarreal has since confirmed it revoked the fan in question's season ticket and underlined its commitment to combatting racism and discrimination.
"Villarreal CF wants to communicate that the club deeply regrets and condemns the incident that happened [Sunday] during the match against FC Barcelona in which a fan threw an object onto the field of El Madrigal," a statement on the club's official website read. "Thanks to the security forces and the invaluable assistance of the Yellow crowd, the club has already identified the author and has decided to withdraw his season tickets, permanently banning his access to El Madrigal stadium.
"Once again our club would like to express its firm commitment to promoting respect, equality, sportsmanship and fair play both on and off the field and our absolute rejection of any act that is contrary to these principles, such as violence, discrimination, racism and xenophobia."
Sunday's incident prompted Alves' Barcelona and Brazil teammate Neymar to begin a 'We're all monkeys' social media campaign to show his support for the 30-year-old, posting a picture of himself eating a banana alongside the caption.
Two own goals and a Lionel Messi strike secured a valuable comeback for Barca on Sunday, with the victory keeping its slim title hopes alive at the end of a difficult week for the club in which former coach Tito Vilanova lost his battle with cancer.