Lowrie, who suffered the injury on May 29 in a collision with Carl Crawford, was in the lineup Saturday, but after an 0-for-5 performance at the plate, the team decided to give the utility infielder a breather.
"I think the rest is good for him," manager Terry Francona said. "The good news is that it wasn't more than a bruise."
Lowrie entered Wednesday's game hitless in his previous 11 at-bats, but he isn't using his shoulder as the reason for his recent struggles.
"I'm not going to make any excuses," Lowrie said. "I'm just going to continue to work to make it better and know that I'm going to be where I should be."
The bruise is still bothering Lowrie, but he is just focusing on regaining the strength in his left shoulder.
"It's not pain free," he said, "but we're working on getting the strength back up and getting it feeling better. Knowing that with what they told me with the MRI results, it's just a matter of getting the strength and the flexibility, and the pain out."