Ellsbury was out of the lineup for Thursday night's game against Clearwater, one day after he went 1 for 3 and played five innings in center field.
He was the designated hitter for Tampa on Monday, then was rested the following day.
Ellsbury is going through a spring training-like progression, which includes sprints and other baseball activities, and is slowly getting his legs back.
The Yankees say Ellsbury is expected to play again Friday. He has been on the disabled list since May 20.