Gardner, who was likely to rejoin the club for its series finale against Tampa Bay, underwent another MRI exam that revealed a further strain in the muscle in his elbow, which has sidelined him since April 18.
Girardi said that Gardner will not swing a bat for at least 10 days, and the club will re-evaluate his status at that point.
"The muscle that he strained, that healed," Girardi said. "He re-strained it, is basically what it is. We are going to go without Gardy for a while here. It's very unfortunate."
Gardner was playing for Triple-A Scranton/Wilkes-Barre on Wednesday night and tripled to lead off the first inning, scored a run and walked twice, but he felt some lingering issues after the game.
Girardi seemed encouraged by the fact that this was not the bone bruise that initially bothered Gardner, and the skipper does not expect it to be a long-term concern.
"The concern is we're not going to have him for a while," Girardi said. "As far as, for me, this being a real long-term thing, I don't think this is, like, a three-month thing. But, unfortunately, I think we're going to be without him for another 15-25 days. And that's unfortunate."
The Yankees have been without Gardner since he was placed on the disabled list on April 19 after apparently injuring himself while making a diving catch in a game against the Twins.
Gardner was batting .321 with five runs scored, three RBIs and two stolen bases in nine games for New York. The Yankees have relied on Raul Ibanez, Andruw Jones and Eduardo Nunez in his absence.
"We miss him," Girardi said of Gardner. "There's no doubt about it. The way he was swinging the bat, his defense, the way he puts pressure on defense. We miss his presence in left field. We've got to find a way to get it done without him."