Sidelined with touches of the flu and a nasty cough that is still spreading through the clubhouse, Jeter was told to keep clear for fear of further contaminating his teammates.
Feeling better on Sunday, Jeter is finally in uniform at shortstop for his first game at the facility.
"It'll be fun," Jeter said. "I haven't even been on the bench. I was sort of quarantined for a while. It looked like it's an exciting atmosphere from what I can tell from the television."
The Subway Series is a stage that has always agreed well with Jeter, the all-time leader with a .385 career regular-season batting average against the Mets.
A good portion of that success was compiled at the Mets' former home, the now-demolished Shea Stadium, land now occupied by a parking lot for the new facility.
Jeter batted .321 (44-for-137) with three home runs and 18 RBIs in 34 regular-season games there, not including his performance during the 2000 World Series, when he belted a leadoff homer on Bobby Jones' first pitch of Game 4.
But Jeter said he doesn't miss the old place -- built in 1964 as a multi-purpose stadium and considered antiquated shortly thereafter -- at all.
"I do not, no," Jeter said. "I'm not trying to be disrespectful. I just didn't like that stadium. The field conditions weren't good. Hitting in a stadium is a lot different than playing defense in a stadium. I didn't look forward to playing there. You liked the atmosphere, but not the field conditions and clubhouse conditions."
Friday and Saturday's contests marked the first games since Interleague Play began in 1997 that Jeter did not play against the Mets, including being forced to spend his 35th birthday watching from the trainers' table with Reggie Jackson as a companion while the Yankees pounded the Mets, 9-1.
"It wasn't fun," Jeter said. "I don't know if you'd say [it was the] worst ever, but I've had some good ones. This wasn't one of them."
The only other time that Jeter did not start a contest against the Mets was on May 22, 2005, one day after he was drilled in the left elbow by a Kris Benson pitch.
Replaced at shortstop by Rey Sanchez, Jeter eventually appeared as a pinch-runner in the eighth inning and scored a run as the Yankees defeated the Mets, 5-3.
"I don't like to miss any games," Jeter said. "It's just one of those things. If I could have played, then I would have played. That's pretty much all you can say. I'm happy I get a chance to play today."
At least 10 members of the Yankees traveling party have been touched by the bug, including coaches and support staff, and manager Joe Girardi said that further tests have been issued as a result.
"We've had some guys where they've taken some throat cultures, and everything has come back fine," Girardi said.
Right-hander Phil Hughes came down with a touch of the bug late Saturday, and Johnny Damon remained out of the lineup for a second successive night with stronger symptoms.
"He's still sick," Girardi said of Damon. "He feels a little weak. He slept better last night but he told me he still felt a little weak. I saw him walking around in a sweatshirt in our clubhouse, which tells me he's not real good."
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.