Encarnacion was struck on the hand by a fastball from Boston's Daniel Bard during the second inning of the Blue Jays' 5-1 victory on Sunday at Rogers Centre.
Toronto's designated hitter briefly remained in the game before being lifted for a pinch-hitter in the fifth inning.
"It's on the back of his right palm," Blue Jays manager John Farrell said. "Basically right below the knuckles of the fourth and fifth fingers. He was in obvious pain, tried to continue on, felt some strength come back in the hand when he was tested on the field.
"But more precautionary than anything with some of the on-site pictures, the floor scan that we can take here, there was enough reason to get him out of today's ballgame and get more concrete evidence."
Encarnacion was one of two Blue Jays players that were hit by Bard on Sunday afternoon. Boston's right-hander also hit Yunel Escobar earlier in the inning and walked six batters in just 1 2/3 innings.
Bard and the Blue Jays have a long-standing history with each other dating back to Spring Training in 2011. That was when the former reliever hit Corey Patterson in the head, which resulted in a lengthy absence for the veteran outfielder.
The 26-year-old Bard also hit Jose Bautista on the hand this spring, but the Blue Jays weren't about to suggest there was any hidden motive. It was clearly a case of a pitcher who wasn't able to command his pitches.
"They weren't intentional," Farrell said. "Yeah, you fear a ball's going to get away from a guy -- and particularly as hard as he can throw. Two fastballs ran up and in, one to Yunel that just clipped him on the right thumb and then obviously the Edwin situation.
"Hopefully this isn't a situation with Edwin that's too long term."
Encarnacion arguably has been the Blue Jays' best hitter this season. The Dominican native is hitting .279 with 17 home runs and 42 RBIs in 54 games.