The Blue Jays handed New York its second straight loss, overcoming an early 3-1 deficit and producing the winning run off Boone Logan (5-3). The New York lead over Boston in the American League East was trimmed to 3 1/2 games.
Adam Lind, who gave Toronto a 4-3 lead in the fifth with a three-run double, had another double to lead off the ninth.
Cory Wade was summoned from the bull pen to face Molina, who hit Wade's third pitch up the middle for the single that ended the game.
Casey Janssen (5-0) retired all six men he faced in the eighth and ninth innings to get the win.