The 30-year-old was injured in Friday night's win sliding into home on Derek Jeter's groundout. A fluoroscope of the ankle late Friday night showed no fracture, but the ankle was sore and swollen, according to ESPNNewYork.com's Wallace Matthews.
The swelling and soreness did not improve by Saturday morning, so manager Joe Girardi decided to give Ellsbury the day off.
Ellsbury, who hit a two-run home run and tripled in Friday's win, leads the Yankees with 64 RBIs.
"My hope is that it's not a long-term thing," Girardi said before Saturday's game. "Adrenaline can carry you a long way. The fact that he wants to try [to play on it] makes me feel better."
MLB rosters expand on Monday, so the Yankees likely won't need to put Ellsbury on the disabled list.
Ellsbury is hitting .286 with 14 home runs in 130 games this season for the Yankees (70-64).
- Chris Mascaro