Chapman struck out Randal Grichuk before exiting in the ninth inning, escorted by a team trainer. He was replaced by Chasen Shreve, who gave up a home run to Aledmys Diaz but finished out the Yankees' 8-5 win.
Chapman has been dealing with the injury since early May.
"Just a little more discomfort than what I usually have been feeling,'' Chapman said through an interpreter.
With the Yankees ahead by four runs, manager Aaron Boone wasn't about to take any chances.
"He said he was fine to continue, but I just didn't want to mess with it,'' Boone said.
Asked what he saw from Chapman that brought him out to the mound, Boone replied, "Maybe just a little more, slower moving, just got our radar up, so we just went out there and checked on him. He said it was just a little sore, 'but I'm fine.' I just decided then, especially with the lead, I thought it was best to get him out."
Boone noted how well Chapman has pitched while dealing with the injury all season.
"I don't think there's much that's changed with it," he said. "Obviously it's something we watch with him very closely and that he's constantly staying on top of, and I don't think today is anything too extreme from what he's been dealing with much of the year."
ESPN's Marly Rivera and The Associated Press contributed to this report.