The 32-year-old was substituted in the 76th minute of the 4-1 defeat at Mestalla after experiencing pain in his left adductor.
He did take part in light training on Friday but Zinedine Zidane, perhaps with one eye on the Champions League clash with Inter on Wednesday, has not named him in the squad for this weekend's game.
Benzema is Madrid's top scorer in the league this season, with four goals in his eight appearances. He has also chipped in with three assists, the most of any Los Blancos player alongside Rodrygo.
There is also no place in the squad for Luka Jovic, who tested positive for COVID-19 on Friday after returning from international duty with Serbia, while Casemiro and Eder Militao – who have been self-isolating following positive coronavirus tests before the international break – are also out.
Sergio Ramos will also be absent after sustaining a hamstring injury in Spain's 6-0 win over Germany. The Madrid captain is expected to be sidelined for at least 10 days.
The is better news regarding Eden Hazard, though, who has been named in the 20-man squad after he tested positive for COVID-19 before the Valencia defeat.
Speaking at his pre-match media conference, Zidane did not want to dwell on the depleted nature of his squad, instead insisting the starting XI he chooses do not take anything for granted against Villarreal.
"What we have to do is be a group," he said. "You're talking about the game tomorrow and on Wednesday it is important for the Champions League, but all games are important, all of them.
"Every time we play, we have to do well. We can't relax, not even for one minute. The opponent demands a lot of you and we know that. We hope tomorrow we'll come out well."
Madrid are fourth in LaLiga, four points behind leaders Real Sociedad, who have played a game more.