Nova said he first felt discomfort -- which he called "stiffness" -- in his shoulder facing his last batter against the White Sox on Tuesday night, when he allowed six earned runs in six innings and took the loss to fall to 11-7.
Manager Joe Girardi removed Nova from the game after he was informed of the injury. Nova was sent back to New York on Wednesday night for tests by team physician Dr. Chris Ahmad, who discovered the inflammation.
"Any time a guy says he has a little stiffness in his shoulder, you're going to worry," Girardi said Wednesday. "We don't think it's anything too concerning, but we've got to make sure."
The Yankees said Nova's treatment will consist of medication and rest, and he will not throw a ball for at least five days.
Nova, who had won 15 straight decisions between June 10 of last season and April 20 of this season, had not been effective since before the All-Star break. Over his past 10 starts, he is 2-5 with a 6.40 ERA, and has allowed 40 hits over his past 29 innings, including five home runs.
Both Girardi and Nova insisted the injury had nothing to do with the right-hander's sudden loss of effectiveness.
"I was pitching my game without pain or anything," Nova said. "I was feeling good. It was just in the last inning, on the last hitter."
Although it has not been officially announced yet, Nova's injury clears a spot on the roster for the Yankees to add CC Sabathia, who is expected to be activated Friday after spending 15 days on the disabled list with left elbow inflammation. Sabathia is expected to start in the opener of a three-game series between the Yankees and the Indians in Cleveland on Friday night.