The club announced Paxton will undergo an MRI on Saturday to determine the severity of the injury.
The 30-year-old hasn't been able to consistently throw a lot of innings because of his lengthy injury history. He labored through his three innings against the Twins, later saying the soreness was affecting his delivery and ability to locate, according to Lindsay Adler of The Athletic.
Losing him would be another huge blow to an already depleted Yankees roster. The team's rotation has been healthy aside from Luis Severino's season-ending lat injury.
After the Yankees' 6-3 victory on Friday, Paxton said he's been feeling pain on the inside part of his knee all season, but the veteran isn't worried about it, according to Brendan Kuty of NJ.com.
Acquired from the Seattle Mariners in the offseason, Paxton has arguably been New York's most important starter so far in 2019. He's 3-2 with a 3.11 ERA and 12.42 K/9 across seven starts.
The Yankees had appeared to be turning a corner on the injury front, too. Catcher Gary Sanchez recently returned from the injured list, and third baseman Miguel Andujar is expected to be activated before Saturday's game in the Bronx. Outfielders Aaron Hicks and Giancarlo Stanton are also inching closer to returning.