Jeter has reinjured his surgically repaired left ankle, which has been fractured twice since last October.
"His ankle is a little sore, so we are probably going to give him a couple of days and make an evaluation," Girardi said.
Girardi was encouraged that the CT scan on Jeter's ankle came back negative Saturday, meaning he has not fractured it again.
With the season ending three weeks from Sunday, Girardi could not be sure that Jeter will play again this year. However, Girardi did say there is no plan yet to shut down the shortstop.
"Not right now," Girardi said.
Jeter, 39, has only played in 17 games this season, batting just .190. The Yankees began noticing earlier this week that Jeter did not appear to be running right, but Jeter never said a word.
"I don't think you will ever get him to concede," said Girardi, who lifted Jeter in the sixth inning on Saturday after watching him run awkwardly down to first base. "I believe that one of the things that have made him great for so long is his ability to fight through things and to find a way to get it done even when it has looked like he might be too nicked up."
In Jeter's place, Eduardo Nunez will be the Yankees' regular shortstop. Nunez is batting .256 on the season.
Jeter began the season on the disabled list after not being able to recover in time for Opening Day because of the fractured ankle he suffered during Game 1 of October's ALCS.
Jeter finally returned just before the All-Star Break in July, but lasted just one game with a quad injury. He returned from that injury for a short period, only to go back on the DL with a calf strain.
"This [year] is probably his worst one ever for him -- to have to live through this," Girardi said. "You could probably go back to when he was 6 years old because he loves to be out there and he loves to compete. And this is the time where he probably likes being out there more than any, and it has been difficult."
Jeter did not speak to reporters before Sunday's game. Girardi made sure to talk to him before meeting with the media.
"I know he is frustrated," Girardi said. "He wants to be out there. It is tearing him up inside. But as much as he doesn't like it and wants to be out there, I think he understands. We are trying to give it a couple of days to calm down."
They know that time is running out on the regular season.
"There is only 20 days left until the playoffs," Girardi said.