Ellsbury fouled a ball off the foot on Aug. 28 against the Orioles and aggravated it stealing second base on Thursday night.
"He's been playing quite a bit since then and playing well," said general manager Ben Cherington. "The soreness increased, so we felt like the right thing to do was to get it looked at again. We did that. We don't have all the information yet, so until we have all the information, I don't think it's the right time to say anything more. I know he wants to play, and we obviously want him to play. That's still our hope, that he'll be playing before too long."
Though the Red Sox will wait until the completion of tests before outlining a time frame, manager John Farrell admitted it could be a while before Ellsbury plays again.
"Yeah, I don't think we're looking at something that's just day to day here," said Farrell. "But before we get into any kind of time frame, I think it's probably best to just -- for all involved here -- is to wait until we get more conclusive evidence and information that might also include a second opinion, which he has the right to and which we support."
Jackie Bradley Jr., the team's No. 2 prospect, was recalled from Triple-A Pawtucket to help fill the void. This is Bradley's third stint with the Red Sox this season, and he started Saturday's game in center field and batted seventh. Starting right fielder Shane Victorino, who will take over Ellsbury's leadoff spot, might play center at times as well.
"Not going to commit to any one definitive approach here," said Farrell. "We'll probably go day to day for the time being, but with as big as this outfield is, felt like the more range, the more ground we can cover with the range available to us, that's the alignment today."
Ellsbury, who is hitting .299 with eight homers, 52 RBIs and 52 stolen bases, was frustrated at having to shut it down.
"Jake's frustrated and he wants to be on the field," Farrell said. "He feels like he can play right now. But at the direction of the medical people, it's like, we've got to be careful of this. I can tell you this -- Jacoby wants to be on the field. He's kind of [angry] he's not here right now to be honest with you."
The navicular bone is the one that Dustin Pedroia suffered a fracture of in 2010, forcing him to miss most of the final four months of the season. However, at this point, the Red Sox haven't detected a break in Ellsbury's foot.
The Red Sox gave Ellsbury an MRI before he returned to Boston.
"Jacoby didn't respond as we might have expected to treatment throughout the course of the game last night," said manager John Farrell. "As a result, we sent him back to Boston to be re-examined by Dr. [George] Theodore and Dr. [Peter] Asnis. [He] went through an MRI that showed -- obviously -- some swelling and inflammation in there to the point where he's been put in a boot.
"We're still in the process of gathering more information, but the MRI showed enough to put him in the boot and immobilize it for now. We're still going through some additional tests, and when that information is more conclusive, I think we'll have a better read on the diagnosis going forward."
Ellsbury was en route to Denver on Saturday and will be examined by Dr. Thomas Clanton on Sunday.
"The more information the better in this case," said Cherington. "We wanted to make sure that happened as quickly as possible so we can make decisions and treatment plans as quickly as possible. Just made sense to do it right away in this case."
The injury to Ellsbury comes at a time when the Red Sox have been clicking on all cylinders. They entered Saturday's game with an 86-57 record and a 7 1/2-game lead in the American League East.