Nova said he felt his shoulder grab as he threw the last four or five fastballs in the sixth inning of his losing effort.
"It was something tight in my shoulder," Nova said. "That was the first time that I've experienced that."
Asked if he was concerned the injury might be serious, Nova replied, "I'm always worried about my arm. I need to be 100 percent. With any kind of injury, you've got feel concerned about it."
Nova said the discomfort is in the side of his shoulder. He is being sent back to New York to be examined by team physician Christopher Ahmad.
"We don't really think it's a big thing, but we want to make sure," Yankees manager Joe Girardi said. "Obviously, we don't think he's going to make his next start. The DL will be determined on what the doctor says. Short-term, there's a little concern, but I don't think it's anything serious."
Girardi said that Nova's situation makes it likely that right-hander David Phelps will stay in the rotation when ace CC Sabathia is activated from the disabled list for a start on Friday in Cleveland.
"We'll have to see as we move forward here if we were to need [Phelps] before that," Girardi said. "Hopefully, we don't."
Nova did not blame his performance, in which he surrendered a grand slam to Kevin Youkilis and a solo home run to Paul Konerko, on the injury.
Nova said that he told Girardi and pitching coach Larry Rothschild about the stiffness in the dugout after the sixth inning, after first consulting with second baseman Robinson Cano.
"I talked first to Cano, because I didn't want to get out of the game," Nova said. "I wanted to keep pitching. He said if I didn't say anything, he was going to go talk to Joe."
Nova, 25, is 11-7 with a 4.92 ERA in 25 starts this season. Girardi said that he did notice at least one pitch late in Nova's start that looked out of place.
"I did see one pitch in the sixth inning that raised my eyebrow; I even asked Larry about it," Girardi said. "He threw one fastball that was 90 [mph]; I said, 'Was that a fastball?' and Larry said yes. Then the next one was 93 or whatever. I've seen him throw plenty of 91 and 92, but it just looked kind of funny to me."