Tony Gwynn Jr. started the rally by reaching base when second baseman Josh Rutledge's throw to first was high off the glove of Justin Morneau. Ben Revere then singled off LaTroy Hawkins (2-1). Chase Utley tied the game with a two- out, RBI single to right field.
Howard, who finished with four RBI, smashed a 2-2 fastball over the left- center field wall off Boone Logan to end the game.
Jonathan Papelbon (1-1) pitched a perfect ninth inning to earn the win.