The Blue Jays used Jose Bautista's 19th homer of the year off Koji Uehara (1-0) in the top of the ninth to forge a 4-4 tie, but the Red Sox responded quickly in the next half-inning against Juan Perez (1-1).
Brandon Snyder singled with one out and went to second when Jacoby Ellsbury coaxed a base-on-balls.
Pinch-runner Jonathan Diaz entered the game for Snyder and Casey Janssen came in to pitch, inducing Victorino to hit a sharp grounder to first baseman Thole. But the ball handcuffed him and bounced off his glove, allowing Diaz to come home with the game-winner.
Synder finished with two RBI for the American League East-leading Red Sox, who took three-of-four in their series with Toronto.
Bautista went 3-for-5 and Jose Reyes also homered for Toronto.
Thole had entered the contest in the third inning after starter Adam Lind exited with back tightness.