Jeter suffered a Grade 1 strain of the quad running out a ground ball on Thursday against the Royals, playing his first game of the season after returning from two fractures in his surgically repaired left ankle.
Jeter was not present at Yankee Stadium on Saturday due to a stomach virus, but he was expected to be on the bench for Sunday's game against the Twins.
Additionally, Girardi said that he held Brett Gardner out of Sunday's lineup to rest his "overall body [soreness], head to toe."
"He's played every day for us," Girardi said. "He's a little bit beat up, but he's available to me. If I can buy him an extra day, I'll buy him an extra day."