Jeter was pulled for a pinch-runner after hitting an RBI single in the sixth inning of a 13-9 loss to Boston on Saturday.
Jeter went to a hospital for a precautionary CT scan. The team said the preliminary results of the scan were negative.
Jeter has missed most of the season while recovering from a broken left ankle in the playoffs last year. He also has been slowed by a strained right calf.
The 39-year-old team captain is hitting .190 in 17 games.
New York general manager Brian Cashman says that if the Yankees weren't pushing for a playoff spot, Jeter could simply take a few days off to rest.