The Magic erased a 17-point deficit in the second quarter and used a 12-point run to put the game away late in the fourth, winning for the seventh time in nine contests.
Indiana, which has lost seven of nine, did not score a basket in the final 5 minutes.
Howard blocked four shots and Anthony Johnson and JJ Redick each contributed 13 points for Orlando.
Mike Dunleavy led the Pacers with 26 points.
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