The team made the announcement after Tuesday night's game. Francis was scheduled to start Wednesday against San Diego. Livan Hernandez will start in his place.
The Rockies said sitting Francis, who is 4-10 with a 5.01 ERA in 24 starts this year, is a precaution and not due to an injury. Francis was on the 15-day disabled June 29-Aug. 6 with left shoulder inflammation.
"We don't feel there's a medical issue; it's precautionary," Rockies manager Clint Hurdle said. "We feel the volume of work since he's been back has been so encouraging and so good that we're in a good place that we don't want to redline it."
Francis acknowledged he had experienced soreness in his shoulder in his last two starts.
"There's some discomfort," he said. "I don't think it's anything serious."
In 2007, Francis emerged as the staff ace after going 17-9 with a 4.22 ERA and helping the Rockies reach the World Series. Francis was 2-1 with a 4.86 ERA in three postseason starts last year.