Encarnacion began experiencing pain in his back during a recent series in Anaheim. He has been receiving regular treatment ever since, but his recent transition from designated hitter to first base likely compounded the issue.
The 28-year-old went through some light hitting drills prior to Tuesday's game against the Rays before being cleared for action.
"He went down and swung the bat early in the cage and felt fine, or felt well enough to be in the lineup tonight," Blue Jays manager John Farrell said. "Any time you're dealing with a back, it's going to be involving any type of movement. Most importantly, though, he felt OK when swinging the bat early before the game."
Encarnacion, who started at DH on Tuesday, will continue to receive regular playing time at first base following the departure of veteran Adam Lind, but his overall workload at the position will be monitored.
The Dominican native entered play against the Rays hitting .262 with 13 home runs and 35 RBIs in 43 games this season.