Jeter originally was in the starting lineup for Friday night's opener, then was scratched and didn't play in the Yankees' 9-1 victory -- on his 35th birthday. Manager Joe Girardi said they were the latest Yankees to get sick, following Chien-Ming Wang, Robinson Cano and Melky Cabrera. He said pitcher Phil Hughes also had a touch of the illness.
"That's on him, man. I told him I could play," Jeter said of Girardi. "That's all his decision."
Jeter sounded congested, and said he had a headache and a cough, but no longer was feverish. Girardi said a team physician recommended that Jeter not start Saturday. Before this year, Jeter had appeared in every Subway Series game.
"I know he really wants to play today and he's not happy about being out of the lineup," Girardi said. "He was really, really sick last night, and Johnny was up all night coughing, and he's got the start of it. Had a little fever when he came in."
Girardi said that including coaches and support staff, nine people had caught the flu. Jeter, he said, had the worst case.
"It's just kind of went around," Girardi said. "It's what happens when you're in a clubhouse and on airplanes together."
He joked that his team had become "our infirmary."
"We're just going to have to wait and see how they are tomorrow," Girardi said. "You can't really come in and just put a lineup up because we don't know how they're going to be."
Fill-in leadoff batter Brett Gardner raised his average 22 points to .303 Friday with a career-high five hits, including his third homer of the season and a triple, then dropped back to .293 with an 0-for-5 night Saturday. Gardner was hitting .265 on June 9 but has hit .375 (15 for 40) since then.
"That's why he's seeing more playing time," Girardi said. "If a guy's really hot, you stick with him and you find days, but that doesn't necessarily mean that one guy's lost his job. We're just riding the hot hand."
Girardi also said the Yankees planned to keep giving Alex Rodriguez days off. After hitting his 564th homer Friday night to pass Reggie Jackson and move into sole possession of 11th place, Rodriguez he had been told down to cut down his practice swings by 75 percent by Dr. Marc Philippon.
"It's not probably clear cut as the Joba rules," Girardi said, referring to restrictions in place on Joba Chamberlain when he first joined the Yankees two years ago.
With Rodriguez's stroke coming back only slowly following hip surgery in March, New York wants to limit to him to five or six games in a row, at least in theory.
"The competitiveness in a player sometimes doesn't allow them to say that I need a day, so it's our job to watch him, and we see or feel that he needs a day, we give him a day," Girardi said.
After he was kept out of the starting lineup for two games at Florida last weekend, Rodriguez went 7 for 22 with two homers and 11 RBIs, raising his average from .212 to .227.
"I think my legs are coming back a little bit. I think like I have more springs," Rodriguez said.
Girardi said the Yankees had been advised by doctors and trainers not to start Hideki Matsui in the outfield, but that he could see action there as part of a late-inning switch.