Paxton will undergo an MRI on Saturday.
"It's just something that's nagging at me enough that I couldn't execute pitches,'' Paxton said. "I'm not real worried it's going to be something long-term. I'm hoping it's something that's just a quick fix."
After getting the final out of the third inning, Paxton left the Yankees' dugout with a trainer and did not return to the game. He threw 64 pitches and allowed one unearned run on two hits in his three innings, striking out one.
"It's been something that's been a little bit nagging throughout the year, not a big deal, but tonight was a little more sore consistently," Yankees manager Aaron Boone said, when asked what led to the decision to pull Paxton. "So we just decided we didn't want to risk anything.
"Hopeful that it's just some soreness that he's been dealing with and tonight on a damp night it was just a little more cranky."
Already with 13 players on the injured list, the Yankees can only hope Paxton won't be sidelined long, if at all. The oft-injured lefty, acquired from Seattle in an offseason trade to be a front-end starter, entered Friday with a 3-2 record and 3.38 ERA in his first six outings for New York.
"Obviously, can't afford to lose him for too long," reliever Adam Ottavino said. "At this point, we're kind of used to it."
Right-hander Jonathan Holder relieved Paxton to start the fourth inning as New York opened its homestand with a 6-3 win.