Ramos tweaked a calf muscle and he will be missing for a few weeks, adding to Zinedine Zidane's injury woes.
The Frenchman is already without Dani Carvajal and Alvaro Odriozola from his defence, and none of those are likely to return in time for this clash.
Nacho could return and partner Raphael Varane in defence - it will be between him and Eder Militao, with Lucas Vazquez standing in at right-back and Ferland Mendy on the left.
Ahead of those, Fede Valverde's long-term injury will likely mean more game time for 35-year-old Luka Modric, alongside Toni Kroos and Casemiro. Zidane has experimented with a No. 10 but he will likely stick with his 4-3-3 here against an excellent opponent.
Up top, Eden Hazard is unlikely to feature and so Karim Benzema will be partnered with Vinicius Jr and Marco Asensio.
Madrid will be looking to get back to winning ways after their 4-1 capitulation at Valencia last time out, but Villarreal are in superb form themselves and this will not be an easy clash.