The club will close part of the stands in its El Madrigal stadium for the Europa League qualifier in late August in a gesture of respect over the racist incident which put Spanish football on the spot.
"For this match Villarreal will close off the area where the incident occurred involving a fan and Dani Alves," the club said in a statement.
"With this gesture it will send a resounding message against racism and xenophobia, making very clear once again the club's position on this type of incident."
A big banner reading "No to racism" will be placed in the closed-off area, the statement said, reiterating club president Fernando Roig's apology for the banana incident.
Fans with regular seats in the closed-off zone will be reseated elsewhere, it said.
Spanish football authorities fined Villarreal €12,000 ($17,000) for the banana incident but stopped short of ordering the stadium to be closed.
Villarreal banned the fan from their facilities and stadium and cancelled his club membership. He was arrested and could face up to three years in jail if convicted of inciting discrimination.
International outrage erupted after the banana landed on the pitch near 30-year-old Alves during the league clash at El Madrigal on April 27th.
Brazilian star Alves won praise for nonchalantly picking up the banana and taking a bite before setting up a goal to help Barcelona come from behind to seal a 3-2 victory.
A week later, Pape Diop, a 28-year-old Senegalese player for Liga side Levante, reacted by dancing when he was targeted by monkey chants during his side's 2-0 victory over Atletico Madrid.
Villarreal finished sixth in the Spanish league this season, entering the playoffs for the Europa League. Their opponents will be drawn on for the two legs of the tie on .