The shortstop left Sunday night's 9-6 win over the Red Sox with tightness in his right hamstring, which he sustained during a feet-first slide into first base after hitting a sixth-inning single.
Jayson Nix -- who replaced Nunez on Sunday -- was the starting shortstop, batting eighth, for Tuesday afternoon's game won by the Yankees, 8-4.
"[Nunez] had an MRI [on Monday], and it came back negative," manager Joe Girardi said. "There's still tightness in there."
Girardi initially said he was "not sure" Nunez would be able to return for Tuesday's nightcap, but the infielder started at shortstop and batted seventh.
With Nunez in the lineup, Girardi shifted Nix to third base and moved Alex Rodriguez from third to designated hitter.
"Nuney's kind of the one that's going to determine who plays, in a sense," Girardi said after Game 1. "Nuney probably never thought he'd have that kind of power in him. He's kind of going to determine who plays in the second game."