Yankees manager Joe Girardi said Nunez is day-to-day after an MRI came back negative.
Nunez hopes to return Tuesday when the Yankees play the opener of a three-game road series against the Colorado Rockies. Girardi said he was not sure if the Yankees will have Nunez for that matchup.
"It started in the first inning," Nunez said. "I had a numbing pain in my stomach. Some food, something like that? I don't even know. I didn't tell nobody, just kept playing. After the second inning, it was worse and in the third inning after I swing, there was a lot of pain. I [went] back to play defense and I couldn't move."
Nunez said it hurt when he swung and made throws. He played the first four innings, including a strikeout in his lone at-bat, before being pulled prior to the start of the fifth.
Nunez told Girardi in the fourth he felt the irritation. After Nunez took swings in the on-deck circle and felt the irritation again, Girardi made the move to pull him from the game.
"You don't want to make that a six-week injury if it can be a couple days," Girardi said.
The Yankees can hardly afford to lose another infielder, as they are already without Alex Rodriguez (hip), Derek Jeter (ankle) and Kevin Youkilis (back). Rodriguez and Jeter are projected to come back after the All-Star break, while Youkilis could be returning in the next few weeks.
If Nunez has to miss a game, that leaves the Yankees rather thin in the infield. Jayson Nix and recent acquisition Chris Nelson would be the shortstop and third baseman, but the team could be in a dire situation if either of them had to leave a game.
Girardi believes the Yankees will be fine with their roster, provided Nunez returns quickly.
"I think for a couple days we're OK," Girardi said. "Sometimes you have to be a little creative."
Nunez has already missed games due to injuries twice this season. After being hit by a pitch on the biceps in Detroit on April 5, Nunez did not start the next two games, although he did enter as a pinch runner in the latter game. On April 12, he was hit by a pitch on the wrist against Baltimore and missed the following two games before returning.
With Jeter sidelined this year, the Yankees have relied heavily on Nunez, who has played in 27 of the team's 30 games. Nunez is frustrated that he keeps getting banged up after receiving this opportunity to be the starter.
"I'm disappointed in myself. I feel bad for myself," said Nunez, who is batting just .200 this season. "How this is an opportunity and it happens right now. But certain things, nothing I can do. Keep working. Doing my thing."
With an off day Monday, Nunez will have some time to heal and potentially make a return against the Rockies.
"I'm happy [the MRI] was negative," Nunez said. "I'll be fine in a few days. I hope maybe Tuesday -- treatment again tomorrow in Colorado."
In addition to missing Rodriguez, Jeter and Youkilis, the Yankees are without center fielder Curtis Granderson (forearm), first baseman Mark Teixeira (wrist), catcher Francisco Cervelli (hand), reliever Joba Chamberlain (oblique) and starter Ivan Nova (triceps).
"Hopefully no one else ends up coming out of games early. It's starting to get out of control now," outfielder Vernon Wells said. "First I was 'OK, a few injuries, it's normal.' Each week something new. Hopefully [Nunez] is going to be OK and we get him back here pretty soon."