David Alaba suffered an ACL injury during the reverse game against the Yellow Submarine at Bernabeu back in December, and the Austria international will not return for Los Blancos until next season.
Aurelien Tchouameni also remains on the sidelines for the La Liga champions due to the foot problem which he picked up in the recent Champions League clash against Bayern Munich.
The France international has an outside chance of being fit for the Champions League final against Borussia Dortmund on June 1, but he will miss the end of the La Liga campaign.
Head coach Carlo Ancelotti has otherwise been able to name a strong squad, while there is a spot for youngster Mario Martin due to Tchouameni's absence.
Alaba, Tchouameni remain on the sidelines for Real Madrid
Andriy Lunin has already been confirmed as a starter between the sticks, but the Ukraine international is widely expected to lose out to number one Thibaut Courtois in the Champions League final.
Courtois has recently recovered from two knee injuries which have both required operations, and he has started the team's last three La Liga matches.
Lunin will be back in against Villarreal, but Courtois is likely to start against Real Betis in the team's final league game of the campaign before featuring against Dortmund.
Ancelotti has also hinted that Eder Militao could start the European Cup final, and the fit-again centre-back could also be in the XI against Villarreal in Real Madrid's penultimate league game of the season.
Ancelotti is set to ring the changes against Villarreal
Real Madrid were confirmed as league champions earlier this month, but Villarreal still have an outside chance of finishing seventh to secure a European spot for next season.
"We approach it as a preparation for the final, we travel with the entire squad and we take it as an important match to have a competitive rhythm and a good attitude and dynamic," Ancelotti told reporters during his pre-match press conference.
"Villarreal play well. The objective is to maintain the good dynamic.
"We have no doubts. I have no doubt what I should do until June 1, which is to prepare everyone as best as possible. And then, make the most correct decision. We have rested and now we have two weeks to put point to the team for the final."
Lucas Vazquez, Fran Garcia, Dani Ceballos, Luka Modric, Arda Guler, Brahim Diaz and Joselu are expected to be among the starters for Real Madrid on Sunday night.
Real Madrid squad vs. Villarreal:
Courtois, Lunin, Kepa; Carvajal, Militao, Nacho, Vazquez, F Garcia, Rudiger, Mendy; Bellingham, Kroos, Modric, Camavinga, Valverde, Ceballos, Guler, Martin; Vinicius, Rodrygo, Joselu, Brahim