In a Triple-A game with Rochester on Friday, Cuddyer was on the basepaths and took a line drive to his left foot. It fractured his second metatarsal.
The Twins learned of his injury early in Friday night's win.
"It kind of puts a damper on things," manager Ron Gardenhire said. "I know how badly he wants to play. That can't be much fun for Mike because he's a gamer. I feel bad for him."
Cuddyer will remain in Rochester on Saturday, and will be flown to Minneapolis on Sunday for further evaluation.
This was Cuddyer's fourth rehab game. Manager Ron Gardenhire had said it was likely Cuddyer would return to the team Monday before the injury occured.
Mark Dent is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.