The 25-year-old was replaced by Liam Hendriks.
Duffy grimaced after the first pitch to Jacoby Ellsbury. Manager Ned Yost and the team's trainer came out to check on him.
Duffy is 8-11 with a 2.42 ERA in 29 appearances this season (23 starts). He began the season as a reliever before moving into the rotation in May.
In four big-league seasons, Duffy is 16-21 with a 3.65 ERA. He missed most of the 2012 and 2013 seasons after undergoing Tommy John surgery on his left elbow.
Kansas City (78-61) entered play on Saturday having won four in a row and held a 2.5-game lead over the Tigers in the AL Central.
- Chris Mascaro