Youkilis has been battling a variety of ailments, and left Monday's game after being drilled high on his back. The third baseman is expected to be back in the lineup Wednesday night in the series finale against the Blue Jays.
Manager Terry Francona says "he's a little stiff" and the team doctors feel it's best to give him a day off.
With Youkilis out, Dustin Pedroia drops to the cleanup spot for the second time in less than a week. Last week, with Youkilis out with a left ankle contusion, Pedroia was 1 for 5 with a home run in a game against the Phillies.