Encarnacion beat out a double-play ball, which allowed Jose Reyes to score, but he began limping just as he reached first base.
The 31-year-old, who is tied for the American League lead in RBIs with 70, admitted to hearing a "pop" in his right leg on the play.
"I wouldn't guess it'd be a quick thing, Blue Jays manager John Gibbons said. "He said he felt something pop in his quad. That's all I know right now. I'd be very surprised if he went on the DL, but I don't know that for sure yet."
The first baseman also has 26 home runs.
Adam Lind came in to run for Encarnacion and stayed in to play first. He was hitless in three at-bats.
The Associated Press contributed to this report.