"Today, it's getting worse with the swing I made in the first inning," Encarnacion said in reference to an RBI single as the Blue Jays extended their win streak to four games.
Encarnacion had three more plate appearances on Saturday, finishing 1-for-3 with a walk and an RBI. He's batting .219 with 12 home runs and 33 RBIs this season.
Encarnacion said he expects to miss Sunday's game "and then see how the pain feels" before deciding when he'll return to the lineup. Toronto hosts the Miami Marlins in a three-game series starting Monday.
Encarnacion, who missed three games in Washington earlier this week with a sore hamstring sustained while stretching for balls while playing first base in Minnesota, said he doesn't remember one particular play that caused any injury to his shoulder.
"It just started after swinging and swinging," said Encarnacion. "Today was the worst part."
Toronto manager John Gibbons said Encarnacion got the cortisone shot "just to calm things down."