Moreno opened the scoring from the penalty spot in the ninth minute and he doubled the lead nine minutes later as Villarreal went into the break with a two-goal lead.
The Spain star had another chance to complete his hat-trick on the hour-mark after Manu Trigueros was fouled in the penalty area, and he converted the ensuing spot-kick.
Chukwueze's introduction on Saturday means the Super Eagles star has now featured in 23 La Liga matches this campaign with a goal and two assists to his name.
Cameroon's Yan Eteki was the second African star at the Estadio Nuevo Los Carmenes but he was an unused substitute for Granada.