"It's giving me a little trouble," Pettitte said. "I've thrown enough innings. There's not any sense in going out and continuing to kill myself now, to push myself through anything."
Pettitte had an MRI exam on his shoulder earlier this month, revealing no major damage. He won his last start on Sunday night, beating Baltimore in the final game at Yankee Stadium.
The 36-year-old Pettitte went 14-14 in 33 starts and threw 204 innings. His 4.54 ERA was his highest since 1999, when it was 4.70.
"We just felt that Andy has got enough innings," manager Joe Girardi said before Wednesday night's game against Toronto. "He was scheduled to start on Saturday if the game meant something. We're going to shut him down and Sidney [Ponson] will make that start."
New York was eliminated from postseason contention Tuesday night when Boston beat Cleveland 5-4.
Pettitte had lost five straight starts before allowing two earned runs in five innings during the win over Baltimore last weekend.
Pettitte, who has 215 career wins, is eligible for free agency after the season. He said he'll go home before making a decision about 2009, but would like to return to New York and open the new Yankee Stadium.
"I just need to get away for a little while," Pettitte said. "I don't want to drag it out. They've pretty much let it be known they'd like to have me back, which is good enough for me."
Pettitte expects the Yankees to have a busy offseason as they work to get back into the playoffs next October.
"I would have to think one of their main concerns is trying to line up the pitching," he said. "That's why, for me, I'll try as hard as I can to figure out what I want to do next year."
Asked whether he would consider a return to Houston, where he played from 2004 to 2006, Pettitte said no.
"I want to play here," he said.
Shortstop Derek Jeter missed his second straight start Wednesday. Jeter, who was hit on the left hand Saturday, came on as a defensive replacement in the ninth inning of Tuesday's game, and was not expected to participate in batting practice, Girardi said.
"We'll take a look at it tomorrow and see how it feels," Girardi said. "If he says he's doing OK, then he'll be in there."
Regulars Johnny Damon and Alex Rodriguez were also out of the lineup Wednesday. Cody Ransom made his second straight start at shortstop, with Wilson Betemit taking over at third base, Juan Miranda playing first base and Chad Moeller getting the start at catcher.