Jeter, on the 15-day disabled list with a calf strain, will instead travel to Tampa to remain under the care of team doctors while he rehabilitates the injury.
It is common practice for players on the disabled list to travel to the team facility in Tampa when the Yankees are on the road. That allows players to be treated by team doctors and rehabilitate injuries in team facilities. If the players remain in New York, they do not have access to Yankees trainers, who travel with the team on road trips.
Joe Girardi said "most" of the Yankees on the disabled list are going to Tampa. He declined to provide further detail on Jeter's rehab program.
"I can't tell you exactly what will happen there. Let's just get him healthy first and then we'll see what happens," Girardi said.
The Yankees placed Jeter on disabled list Tuesday evening after he suffered a calf strain on Monday night in their loss to the Indians.
The DL stint puts Jeter's pursuit of 3,000 hits on hold for at least two weeks. Jeter, just six hits shy of the 3,000 club, is eligible to come off of the disabled list on June 29 -- three days after his 37th birthday.
Jeter is on the DL for the first time since he suffered a dislocated left shoulder on Opening Night 2003, an injury that cost him the first 36 games of the season.
The Yankees captain made it clear that he wasn't happy with the move to the disabled list on Tuesday -- but he understood it.
"I'd rather not go on (the DL). In my opinion if I could play in four or five days, or six days or seven days, it's better than waiting 15," a subdued Jeter said. "I haven't made a living on the disabled list."
The DL designation also decreases the likelihood that Jeter will reach the 3,000-hit plateau at home.
On June 29, the Yankees will play the second game of a three-game series at home against the Milwaukee Brewers, and then head off on a six-game road trip, three at Citi Field against the Mets and three against the Indians in Cleveland.
"Well, I guess the timing wasn't very good," Jeter said on Tuesday. "It's frustrating but even if I wasn't at this point I'd still be frustrated. I don't like not to play. Whether I'm going for 3,000 hits or 100 hits, it really doesn't make a difference to me. I'd rather be out there playing. I'm disappointed because I feel a lot of people are looking forward to getting the opportunity to see it, especially here this week. I feel bad for that. But hopefully in time that day will come."
Jeter is batting .260 with two home runs and 20 RBIs this season. His on-base percentage is .324.
Nunez, who played nine error-free innings in place of Jeter at shortstop, had an RBI single in the Yankees' 12-4 win over the Rangers on Tuesday. Brett Gardner, who replaced Jeter in the leadoff spot on Tuesday, went 3-for-4 with three runs scored and reached base four times in the Yankees' rout.
Nunez was penciled in at shortstop for the Yankees on Wednesday night against Texas. With the Yankees facing Texas lefthander Derek Holland, Gardner was benched. He was replaced in left field by Andruw Jones. Right fielder Nick Swisher was batting leadoff, his first start in the top spot since 2008 when he was with the Chicago White Sox.
"Just the on-base percentage he has against left-handers this year and his career, and he's not upsetting (Curtis) Granderson and the other guys," Girardi said of his reason for batting Swisher first and leaving Granderson in the two hole.
Swisher was up for the job.
"I figured I hit in every spot of the lineup, might as well do this now," Swisher said said before going 1-for-3 with two walks and a run scored in the Yankees' 12-4 win. "Like Jeet said, the only thing that matters is the first at-bat then it folds into one big lineup."
Meanwhile, Francisco Cervelli was behind the plate for the seventh time in eight games because Russell Martin's back was still sore. Girardi is waiting for Martin to tell him the back is healed before putting him back in the lineup.
Ian Begley is a regular contributor to ESPNNewYork.com. Information from ESPNNewYork.com's Wallace Matthews and The Associated Press was used in this report.