The veteran slugger said he was feeling better on Wednesday, but with an off-day coming on Thursday, it made sense to sit another day to avoid the hamstring becoming a more serious issue.
"I just want to make sure, I don't want to lose like 15 games," Encarnacion said. "I'd prefer to lose two or three games and come back again. If I feel something can be worse, I'd prefer to lose two or three games."
The news shouldn't come as a total surprise because Encarnacion has been playing almost every day at first base. Toronto went into the year hoping to have Encarnacion split his time at first and designated hitter, but injuries elsewhere made that an impossible goal.
Jose Bautista went through a stretch of six weeks where he wasn't able to play the field because of a sore shoulder. That meant all of his at-bats had to come as a DH, which forced Encarnacion into the field. Encarnacion usually has trouble staying healthy under those circumstances, and it appears as though the workload has caught up to him.
The good news is that Bautista made his return to right field on Tuesday afternoon and he's expected to remain there barring any setbacks. That will allow Encarnacion to DH on at least a semi-regular basis with Justin Smoak getting more playing time at first.
Encarnacion was available to pinch-hit during the Blue Jays' Interleague series in Washington and estimated that he can run at about 80 percent. The bigger issue is in the field at first when he is forced to stretch for errant throws from across the diamond.
"That's going to help me, now Jose can play right field and I can be more of a DH until I can get 100 percent and go back to first," Encarnacion said. "When I'm hitting, I don't feel it. I won't be running 100 percent, but I can run 80, so I feel quite good."
Gregor Chisholm is a reporter for MLB.com. Read his blog, North of the Border, follow him on Twitter @gregorMLB and Facebook, and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.