Chad Gaudin will start Wednesday against the Blue Jays instead, with Pettitte now lined to pitch on Monday against the Angels in Anaheim.
"He's gone hard for us," Girardi said. "It is a concern. We feel that skipping him in this turn will knock this out and give him a good chance to re-energize himself. He says he feels good right now, and we want to keep him that way."
Pettitte, 37, has been one of the Yankees' most reliable starters this season, faring 13-6 with a 4.14 ERA in 29 starts.
But the veteran began to lose some of the sharpness of his stuff against the Orioles, running through 103 pitches in five innings and taking a no-decision. His cutter went flat, and Pettitte complained of what seemed to be a dull ache in his shoulder.
"I really didn't feel like I was hurting that much," Pettitte said. "I've thrown every day since the start, and it doesn't hurt right now. I just feel like it would be best to try and skip the start and nip it in the bud right now before it gets any worse. ...
"I definitely don't want to be standing on the mound in the postseason or a game at the end of the year that might matter a little more with my arm aching."
Last Sept. 21, Pettitte made the final start at the old Yankee Stadium, summoning every ounce of his remaining energy to log a victory in an emotional game.
It was the highlight of an otherwise disappointing second half for Pettitte, who had lost his last five starts leading into that game.
Pettitte said that he feels nothing like he did then, recalling how it hurt to do anything then, and how he feels no pain. Pettitte said he has thrown every day since his last start and that he believes he could make his usual turn, but is not sure if his stuff would be sharp.
"I really know that I could make my start Wednesday, but I don't know if it would fatigue out again," Pettitte said. "They just think with the rest and skipping a start that it should clear it up."
Girardi said that he believes the time off will help Pettitte, and he feels that the veteran is being forthcoming with the state of his shoulder, but the Yankees will still watch the crispness of his next start closely.
"A lot of times when you have what Andy has, it doesn't say you can't pitch," Girardi said. "You're not quite as sharp. You can see those signs, so we'll watch very carefully Monday. If we feel he starts to fatigue in the fourth or fifth inning, we're going to get him out."
Pettitte passed all the Yankees' manual strength examinations and threw a light bullpen session on Monday at Yankee Stadium, the short variety that Roger Clemens used to call his "Williamsport."
The plan is that Pettitte will toss bullpen sessions on Friday and Saturday in Seattle before his start on Monday. Pettitte said that he has not required a cortisone injection and expects that the rest will do the trick, however, it is comforting to know that the option is there.
"It's been such a good year, as far as my arm and how it's responded after last year," Pettitte said. "Obviously, it's disappointing that it started aching a little bit my last start, but ... I hope it feels great."
Girardi has been hesitant to talk too much about the playoffs, wanting his club to clinch first. But it is likely to figure that Pettitte would be one of the Yankees' starters in the American League Division Series, likely slotting in the rotation with CC Sabathia and A.J. Burnett.
That looming assignment makes his recovery from this slight setback all the more important.
"It's kind of what I've talked about all year," Girardi said. "One of the most important things is health. You've got to keep your players healthy and you've got to watch them. A lot of things can change if you have a couple of injuries."