The inter-league "subway series" was shortened to two games after Friday night's contest at Yankee Stadium was rained out and no make-up date was scheduled.
Wright's homer, his eighth this season, came with no outs in the top of the seventh inning, when the Mets scored three times for a 3-2 advantage.
Jose Reyes had two hits, one a solo homer in the seventh. Four players drove in one run apiece, including Carlos Beltran, who also had three hits.
Reyes and Carlos Delgado had two hits for the Mets, who had lost three of four.
The winner was starter Johan Santana (5-2). Closer Billy Wagner earned his ninth save.
The Yankees, who have dropped four of five, got three hits -- one a two-run homer -- from Derek Jeter. Both Bobby Abreu and Jason Giambi hit solo homers among their two hits.
The losing pitcher was Andy Pettitte (3-5).