Mark Kotsay, making his return to Atlanta for the first time since the Braves traded him to the Red Sox last August, got the start in center and batted seventh.
"I just got hit in a weird spot, and it swelled up on me pretty good in the joint," Ellsbury said. "It's basically just the range of motion, it just swelled up in the joint pretty good. I must have just hit it in the right spot. I'm just going to ice it and get that swelling out, and it should be fine."
Ellsbury hopes to be back in the lineup on Saturday afternoon.
Don't be surprised if Ellsbury enters Friday's game in the late innings.
"I think he's available," said Red Sox manager Terry Francona. "I don't know that we really wanted to start him and let him swing four times. Hopefully, we'll have a lead and we'll put him in for defense."
Ellsbury is hitting .307 to go with 31 stolen bases.
Ian Browne is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.