The moves were made before Monday's game against Kansas City. To make room on the roster, shortstops Pedro Florimon and Jorge Polanco were sent to the minors -- Florimon to Triple-A Rochester; Polanco to Class A Fort Myers.
Plouffe, who is hitting .241 with five homers and 38 RBIs this season, missed 14 games after injuring his rib cage against Detroit on June 14. Nunez, who just finished a four-game rehab assignment with Rochester, also missed 14 games after straining his right hamstring in the same game.
Florimon went 0 for 11 in eight games since he was called up, dropping his career average to .204 in 624 major league at-bats.
Polanco went 2 for 5 over four games after making his major league debut.
The Associated Press contributed to this report.