A right hip problem will keep the left-back out of the meeting at the Estadio de la Ceramica.
The issue further restricts Quique Setien's senior options in defense, with Samuel Umtiti ruled out of the match due to a left knee injury.
Junior has featured 20 times in all competitions for Barca this season, starting just once since the league resumed last month following its suspension amid the coronavirus pandemic.
Defending champions Barca will be seven points adrift of top spot at kick-off if leaders Real Madrid beat Athletic Club earlier in the day.
Villarreal are unbeaten since LaLiga returned, winning five of their six games, and are just three points behind fourth-placed Sevilla in the final Champions League qualification spot.