Nunez has been sidelined with a strained left oblique since May 5. It has not been determined how long Nunez will play in Trenton; the Thunder hosts Double-A Reading in a 7:05 p.m. ET contest on Thursday.
Nunez opened the season as the Yankees' everyday shortstop in Derek Jeter's absence but was limited to 27 games, batting .200 with no homers and four RBIs. Girardi said that injuries have made the season a rough one for both Nunez and catcher Francisco Cervelli.
"That probably adds to their frustration," Girardi said. "It was a chance to play every day, a chance to kind of validate that you're an everyday player, and they've been hurt most of the time."
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.