Norway international Odegaard has featured just twice for Madrid in all competitions since the start of December, and Wednesday's clash with third-tier Alcoyano appeared to represent a chance for him to receive some rare minutes.
However, the 22-year-old was not included on the 20-man list for the match at El Collao.
Varane and Modric, who have missed just one game each this season, were granted a rest by Zidane, with Castilla duo Victor Chust and Antonio Blanco called up instead.
Ramos played through discomfort experienced in the warm-up during the Supercopa de Espana defeat to Athletic Club last week and did not train with his team-mates on Tuesday.
Rodrygo and Dani Carvajal are also unavailable due to injury.