An MRI revealed the mild strain, the latest setback in a year already full of injuries for the team captain.
"It's frustrating," Jeter said after the Yankees lost 6-3 to San Diego. "It's terrible. The whole season has been a nightmare."
The 38-year-old Jeter did not play the last two days against the Padres.
"I'm not so sure what we're going to do," Yankees manager Joe Girardi said.
Before the game, Girardi said he didn't know if this injury came about because of a strained right quadriceps that landed Jeter on the disabled list from July 12 until being activated last Sunday.
It appeared that Jeter took an awkward step while making a play in Friday night's 7-2 loss. He also had an awkward slide into third base.
Jeter is hitting .211 (4 for 19) with one home run and two RBIs.
Jeter broke his left ankle in the AL championship series in October and opened the season on the DL.
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