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.
Ray Liotta sues skin care company over use of likeness
NBC reportedly holds celebs hostage to Jimmy Fallon's show