Anthony Bass will get the start in Kelly's place against the Brewers.
San Diego manager Bud Black said that Kelly's right arm has not "bounced back the last couple of starts to where we felt one more start would be worth it."
Kelly, who missed three and a half months of the season with a strained right elbow while pitching in the Minor Leagues, was scheduled to pitch later this month in the Arizona Fall League to pick up innings that he missed when he was on the disabled list as well as work on a changeup.
But now the goal for the 22-year-old will be to have a restful offseason with an eye on reporting for Spring Training healthy and competing for a spot in the starting rotation.
"For Casey, the most important thing is 2013," Black said. "The 30 or 40 innings he would have pitched [in the Arizona Fall League] are not as important as 2013."
Kelly was 2-3 with a 6.21 ERA in six starts after joining the team on Aug. 27. He began the season with Triple-A Tucson and made two starts before going on the disabled list in April.
"Even though the volume wasn't there, we saw some good quality," Black said.
Bass, who made 14 starts earlier this season before landing on the disabled list in June with an inflamed right shoulder, will likely throw between 40-60 pitches, Black said. From there, Black said the Padres will cover the rest of the game with relievers.
"He's not stretched out like some starting pitchers, but he's got a starter's mentality," Black said of Bass.