Owner Jess Jackson announced the decision Friday, adding that the 3-year-old sensation will return to the races in 2010.
Earlier, Jackson had said Rachel Alexandra would not run in the Breeders' Cup Classic on Nov. 7 at Santa Anita because he did not like to run his horses on a synthetic surface.
Rachel Alexandra completes the year with an 8-for-8 record, including wins against boys in the Preakness Stakes, the Haskell Invitational and the Woodward Stakes against older horses.
The chestnut filly is a leading contender for Horse of the Year. Rachel Alexandra will spend the rest of the year at Churchill Downs.