The Phillies trailed 4-3 in the eighth but managed to push across the tying run when John Mayberry singled, went to second on a wild pitch and scored when David Hernandez threw wildly to first on a Domonic Brown grounder.
After Chase Utley was intentionally walked, Howard hit a sharp liner into right field to chase home Pierre and hand Philadelphia a win in the rubber match of a three-game series.
Jonathan Papelbon (3-4) collected the victory after tossing a scoreless top of the ninth. Phillies starter Cliff Lee surrendered four runs over eight innings.
Paul Goldschmidt, Chris Johnson and Stephen Drew each homered for Arizona.