Howard drove Yhency Brazoban's first pitch deep into the seats in right-center, the ball sailing an estimated 453 feet.
The homer was Howard's eighth of the year.
He also hit a two-run shot off Brazoban (2-7) in the 10th inning at Philadelphia on July 19 to give the Phillies a 5-4 win.
The Phillies learned shortly before the game that slugging first baseman Jim Thome is expected to undergo elbow surgery on Tuesday and miss the rest of the season.
Ugueth Urbina (2-0) pitched a hitless eighth inning for the win.
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