The team flew through a large thunderstorm system, and manager Joe Girardi said the resulting turbulence was "as bad I've seen."
"The first half an hour was OK, then the next 45 minutes was knuckleball express," Girardi said. "We got quite a light show, and it wasn't below us. The lightning seemed like it was inside the airplane. Needless to say, no one really slept after that."
New York arrived at its hotel about 6 a.m. - the time some players get to the clubhouse spring training.
"They were thinking about taking the bus right here," Girardi joked at the ballpark.
Jeter, starting his 20th season, rested as the Yankees played on artificial turf, and Dean Anna started at shortstop. Second baseman Brian Roberts and designated hitter Alfonso Soriano also did not start.