Jeter, 39, was on the disabled list to start the season as he continued to recover from a left ankle fracture suffered in Game 1 of last year's American League Championships Series.
He made his 2013 debut in mid July but has appeared in just 17 games, hitting .190 with one home run and seven runs batted in.
Jeter was pulled from Saturday's game after New York Manager Joe Girardi said he didn't like the way Jeter was running. Further examinations, however, didn't indicate a problem.
While Jeter is formally on the 15-day disabled list, the Yankees said they were ending Jeter's season to reduce the chance of further damaging the ankle.
"This is what's best for Derek," Yankees General Manager Brian Cashman said. "Something's going to give at some point the more we run him out there."
Over 19 seasons -- all with the Yankees, Jeter has hit .312 with 3,316 hits, 256 home runs and 1,261 RBI. Jeter's hit total is ninth most all-time in the major leagues.
The Yankees are wrapping up a four-game series in Baltimore Thursday before heading to Boston for a three-game set against the AL East-leading Red Sox.