Jeter is guarding a sore right oblique that has bothered him for the better part of a week, while Matsui felt his right hamstring tighten up while running out a ground ball in the second inning on Tuesday against the Blue Jays.
"We have tough guys that are willing to play when they're nicked up," Yankees manager Joe Girardi said. "Sometimes the nick is something that turns into something big and you have to be cautious. But the feeling is that it's not going to be like this all year. I really believe that we're going to stay healthy and stay strong."
Girardi said that he would stay away from using Jeter under any circumstances and that he was not sure the shortstop would be able to play on Thursday either, perhaps moving his target return date to Friday against the Twins in New York.
"I'd rather take two days here than two or three weeks," said Jeter, who fielded ground balls during batting practice but will not swing until Thursday.
Girardi said that the Yankees had more encouraging news on Matsui, with tests showing no blood in his hamstring. Matsui said before the Yankees' lineup was released that he expected to be in the game.
"I feel like I could play," Matsui said through an interpreter. "It's just a matter of how I feel on the field, but I feel pretty good."
Matsui could be used as a pinch-hitter on Wednesday if needed, Girardi said, but that could necessitate a pinch-runner.
Johnny Damon started as the designated hitter and led off on Wednesday, with Ramiro Pena making his second straight start at shortstop and batting eighth.
The Yankees are also expected to be without left-handed reliever Phil Coke, who felt his back tighten while stretching before Tuesday's game.
But they could be getting Brian Bruney back soon. The reliever threw 25 fastballs in a bullpen session on Wednesday as he returns from a strained flexor muscle in his pitching elbow, and Bruney could be activated next week without a Minor League rehabilitation assignment.
"It felt like I wasn't far from pitching in games," Bruney said. "It felt good. The main thing is just getting my feel back. I'm definitely not throwing it where I want to right now, but it wasn't bad. I don't know how you can get encouraged by still being on the DL, but it wasn't bad."
Also Wednesday, manager Joe Girardi said right-hander Chien-Ming Wang would make at least one more Minor League rehab start, although the date and location have yet to be decided. Wang allowed three hits in six scoreless innings for Triple-A Scranton/Wilkes-Barre on Tuesday.
"We need to see more consistency out of his sinker," Girardi said. "I think that's the big thing, but he was definitely better."
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.