Encarnacion experienced pain in that area earlier in the season and was able to work through it, but on Sunday, manager John Farrell had seen enough and lifted him for precautionary reasons.
"He couldn't finish his swing as normal as today progressed," Farrell said. "It was clear we had to get him out of the game."
Encarnacion went 0-for-2 with a walk and scored a run in the first inning on a sacrifice fly by Adam Lind.
Farrell said the team isn't ready to shut Encarnacion down for the year, despite having just three games remaining on the schedule.
The Blue Jays will reevaluate Encarnacion on Monday, when they open up their final series of the year at home against the Twins. From that point, they will determine a plan.
"We will certainly be cautious with this, given where we are in the season," Farrell said.
Encarnacion is second in the Major Leagues with 42 home runs, trailing only Josh Hamilton and Miguel Cabrera, who are tied for the lead with 43.
Colby Rasmus replaced Encarnacion and struck out during a seventh-inning at-bat against lefty Boone Logan.
Toronto split the four-game set.