Ellsbury was not able to come up with the sinking Colby Rasmus liner, which was scored as a RBI triple and opened the door for a five-run first inning against right-hander Ivan Nova.
Girardi said that there have been no tests performed, but that he only left Ellsbury in the game because the Yankees were running short on position players. Girardi hopes to be able to put Ellsbury's name in the lineup Friday when the Yanks open a three-game Interleague series against the Braves at Turner Field.
"I hope we do [have him], but I can't tell you for sure," Girardi said.
Ellsbury missed nearly two months earlier this season with a right knee sprain. He entered Wednesday batting .278/.339/.375 with six homers, 27 RBIs and 17 stolen bases in 78 games.
Before Wednesday's game, the Yankees returned right-hander Michael Pineda from rehab and reinstated him from the 15-day disabled list to start the series finale. They also recalled right-hander Nick Goody from Triple-A Scranton/Wilkes-Barre.
In corresponding moves, left-hander Chris Capuano was designated for assignment -- the fourth time he has been designated this season, and the third this month alone -- while right-hander Nick Rumbelow was optioned to Triple-A.
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch, on Facebook and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.