Then in the next frame, Mike Baxter launched a ground-rule double with one out against David Robertson (3-1) and pinch-hitter Jordany Valdespin drew a walk.
Valdespin, however, moved to third on the play and came home with the decisive run when Murphy followed by lacing a solid hit to center field.
Brandon Lyon (2-2) earned the decision in relief of Jonathon Niese, who held the Yanks to one run on eight hits over seven innings.
Bobby Parnell hurled a scoreless ninth for his eighth save as the Mets took the opener of a four-game home-and-home interleague rivalry series.
Hughes surrendered just one run on four hits over seven full frames for the Yankees.
Jayson Nix provided their only RBI.