The announcement comes in the wake of O'Neill receiving a 45-day suspension from the New York State Gaming Commission after one of his horses tested positive for a banned drug in a claiming race last year.
The move by New York officials set off a Breeders' Cup provision that no trainer can enter a horse if he or she has been found to have violated "a racing regulation prohibiting the possession or use of any substance listed" as a Class 1 or Class 2 medication during the 12 months preceding the championships.
O'Neill's horse tested positive for Oxazepam, a sedative, following a claiming race at Belmont Park on June 2, 2013. O'Neill's suspension is scheduled to begin on Nov. 3.
O'Neill told the Daily Racing Form that he will not appeal the Breeders' Cup decision.
O'Neill had been expected to have as many as five horses participate in the Breeders' Cup, including sprinter