Pettitte gave up two runs on eight hits in six innings to halt a personal four-game skid.
The Yankees broke the game open with an eight-run fifth, during which they sent 13 men to the plate. Matsui, Moeller and Abreu all had two-run singles in the inning.
Duncan's homer came in the second and gave New York a 3-1 lead.
Erik Bedard (3-3) allowed nine runs on eight hits in 4 1/3 to take the loss. Seattle has dropped four straight.
The Yankees were without Manager Joe Girardi, who was suspended for one game and fined for his tirade directed at umpire Chris Guccione during the ninth inning of New York's win over Baltimore Thursday.