Encarnacion was forced to depart Sunday afternoon's game against the Yankees in the seventh inning because of discomfort in his neck and shoulder.
The Blue Jays remain optimistic that Encarnacion will be able to play in at least one of the club's final two games, but it's too early to know for sure.
"Hopeful, but he's not ready to go today," manager John Farrell said. "It's the classic day to day."
Encarnacion entered play on Monday night just one home run behind Detroit's Miguel Cabrera and Texas' Josh Hamilton for the American League lead in homers, with 42. He also ranks tied for third in RBIs (110), fourth in slugging (.557) and OPS (.941).
The Dominican native has been even more impressive with two strikes. He leads the Majors with 21 homers once reaching that plateau in the count.