"Eddy's still a little banged up; his wrist is hurting today," manager John Gibbons said Tuesday.
The Blue Jays slugger's injury is still considered minor and will be monitored on a day-to-day basis.
Encarnacion is hitting .276 with 36 home runs and 104 RBIs in 139 games. His absence from the lineup makes way for Kevin Pillar.
Pillar has had trouble adapting to Major League pitching over 21 games, batting just .172 with a home run and seven RBIs. He will be batting ninth as the club's designated hitter, with Adam Lind taking over duties at first base.