The Yankees said that Stanton will undergo an MRI exam Tuesday night to determine the severity of the injury.
Stanton suffered the injury after sliding into third base in the first inning. Initially, the slugger appeared to sustain a hand injury after Blue Jays pitcher Clayton Richard, who was fielding on the play, stepped on Stanton's left hand.
Stanton remained in left field in the second and third innings, but Brett Gardner eventually replaced him as a pinch hitter in the fourth inning.
Stanton was playing in his sixth game since returning from the injured list. He appeared in the Yankees' first three games this season before being placed on the 10-day IL with a strained left biceps. He wound up missing about three months after injuring his shoulder in April.
Stanton was 1-for-1 with a single before departing the game. Gardner went 0-for-3 in place of the All-Star outfielder.
The Yankees defeated the Blue Jays 4-3 and moved to 51-28 this season. New York leads the Tampa Bay Rays by 5 1/2 games in the AL East standings.