Modric was still named in Madrid's bloated squad for the trip to Tallinn, but the 32-year-old has to settle for a place among the subs, as a three-man midfield of Toni Kroos, Casemiro and Isco is instead preferred.
Lopetegui, taking charge of his first competitive game since replacing Zinedine Zidane in June, sticks with a settled back four of Dani Carvajal, Raphael Varane, Sergio Ramos and Marcelo, with big-money signing Alvaro Odriozola nursing a minor groin injury.
Thibaut Courtois is not involved following his arrival from Chelsea last week, meanwhile, so Keylor Navas will start between the sticks, and further forward it is down to Gareth Bale, Karim Benzema and Marco Asensio to lead the line in Los Blancos' first match without Cristiano Ronaldo.
Elsewhere, Koke and Saul Niguez partner the aforementioned Rodri and Lemar in midfield, while Stefan Savic and Diego Godin link up in the heart of a formidable defence that is further protected by Jan Oblak.
Real Madrid: Navas; Carvajal, Varane, Ramos, Marcelo; Kroos, Casemiro, Isco; Bale, Benzema, Asensio
Subs: Casilla, Lunin, Nacho, Modric, Vazquez, Llorente, Mayoral, Ceballos, Valverde, Vinicius, Reguilon, Sanchez
Atletico Madrid: Oblak; Juanfran, Savic, Godin, Lucas Hernandez; Koke, Rodri, Saul, Lemar; Diego Costa, Griezmann
Subs: Adan, Alex, Luis, Arias, Gimenez, Thomas, Gelson, Vitolo, Olabe, Kalinic, Correa
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