The shortstop was in his customary leadoff spot in the initial lineup against the Mets on Saturday. But a new order was posted about 90 minutes before the game with left fielder Brett Gardner in the top spot.
The Yankees said Jeter injured his heel running the bases in Friday night's loss and was receiving treatment.
Also, Alex Rodriguez was the designated hitter. He played third base Friday and Yankees manager Joe Girardi wanted to be cautious. Rodriguez missed four games with hip tendinitis.
Ramiro Pena moved from third base to shortstop, and Kevin Russo was inserted at third.