Banuelos -- who entered the season ranked as the club's No. 1 prospect by MLB.com -- has been placed on the DL retroactive to Saturday with a sore left elbow, while Nunez is on the shelf retroactive to Sunday with a sore right thumb.
The DL stint is the second of the season for Banuelos, 20, who previously battled a back injury. Banuelos is 0-2 with a 4.50 ERA in six starts at Triple-A.
After Nunez committed four errors in 20 games, the Yankees optioned the utility man to the Minors on May 11 with the intent of having him focus on playing shortstop. Nunez had three hits in 13 at-bats (.231) at Triple-A.