The former Real Madrid forward has struggled for form in the second half of his first campaign at Stamford Bridge, scoring 15 goals in 47 appearances for the Blues having joined for a club record £60 million ($80.5m) in the summer of 2017.
Morata has previously scored 13 goals in 23 appearances for La Roja, but the likes of Diego Costa, Iago Aspas and Rodrigo Moreno have been preferred by head coach Julen Lopetegui.
The former Real Madrid and Juventus striker took his omission well, tweeting minutes after the announcement that he wishes Spain "the best of luck at the World Cup" and that he'll be "supporting and encouraging the team until the end always".
Muchísima suerte en el Mundial!! Desde ya estaré apoyando y animando hasta el final como siempre!! — Álvaro Morata (@AlvaroMorata) May 21, 2018
The 2010 winners have followed England's lead in naming their 23-man squad well ahead of time rather than an extended provisional roster as they look to win their fourth major tournament in a decade.
David de Gea is set to start in goal after another fine season for Manchester United, with Clasico rivals Sergio Ramos and Gerard Pique the established centre-back pairing.
Arsenal's Nacho Monreal is preferred to Chelsea's Marcos Alonso to provide competition for Jordi Alba at left-back while Real Madrid duo Dani Carvajal and Nacho will fight it out for a place on the opposite flank.
Sergio Busquets, Andres Iniesta and David Silva are likely to be Lopetegui's first-choice midfield trio, with Isco deployed slightly further forward.
Most of the 32 nations who will feature at Russia 2018 have named their squads already, with Spain last out the blocks of the big guns following Belgium's announcement earlier on Monday morning .
Spain's full 23-man squad:
Defenders: Jordi Alba (Barcelona), Cesar Azpiliqueta (Chelsea), Dani Carvajal (Real Madrid), Nacho Fernandez (Real Madrid), Nacho Monreal (Arsenal), Alvaro Odriozola (Real Sociedad), Gerard Pique (Barcelona), Sergio Ramos (Real Madrid)
Midfielders: Thiago Alcantara (Bayern Munich), Sergio Busquets (Barcelona), Andres Iniesta (Barcelona), Isco (Real Madrid), Koke (Atletico Madrid), Saul Niguez (Atletico Madrid), David Silva (Manchester City)