Fort Larned ran the race of his life, leading all the way to win by a half-length over Mucho Macho Man.
The highly anticipated Classic was strictly a two-horse race to the finish.
Mott's trio of Flat Out (third), Ron the Greek (fourth) and To Honor and Serve (10th) came up short.
Mott, unlike Baffert, didn't leave empty-handed. Royal Delta successfully defended her title in the $2 million Ladies' Classic on Friday, as one of only four favorites to win in 15 races over two days.
The spotlight belonged to an unheralded horse named for an old post in Kansas that protected the Santa Fe Trail, a jockey who rides in racing's minor leagues, and a low-profile trainer.
"The prestige of winning this race in front of the world is unbelievable," jockey Brian Hernandez Jr. said.
He celebrated his 27th birthday with the biggest victory of his career. Trainer Ian Wilkes could say the same.
"Fort Larned just gave us the greatest birthday present ever," said Hernandez, who was the leading rider this year at Ellis Park and Kentucky Downs.
Fort Larned ran 11/4 miles in 2 minutes, 0.11 seconds in the showcase race of the two-day world championships at Santa Anita that was shown in prime time for the first time. The 4-year-old colt paid $20.80 to win. Wilkes had never won such a big race.
Baffert went 0 for 9 on the weekend, with Game On Dude failing to deliver the Hall of Famer a first-ever win in the Classic. It was the end of a bummer year for him after surviving a heart attack in March and finishing second in each of the Triple Crown races.
Mucho Macho Man was second and Flat Out was third.
Upsets dominated six of the day's nine races, with Little Mike pulling off the biggest stunner at 17-1 odds in the $3 million Turf.
Little Mike, who won by a half-length under jockey Ramon Dominguez, paid $36.60, the highest win price for this year's event.
Rosie Napravnik joined Julie Krone as the only female jockeys to win a Breeders' Cup race when she guided 6-5 favorite Shanghai Bobby to a head victory over He's Had Enough in the $2 million Juvenile.
"As long as you've got the horse underneath you, you can get the job done," said Napravnik, who started her career riding under her initials A.R. so no one would realize she was a woman.
Shanghai Bobby dug in along the rail after it looked as if he was beaten in the stretch, setting himself up as the winter book favorite for the Kentucky Derby. The colt improved to 5-0 under trainer Todd Pletcher, who went 1 for 10 on the weekend.
"He's got everything you want. He's fast and courageous," Pletcher said. "He's handled everything we've thrown at him, from 41/2 furlongs to 11/16 miles. He just keeps coming."
Wise Dan, the 9-5 favorite in the $2 million Mile, came through with a 11/2-length victory, covering the distance in a track-record 1:31.78. He paid $5.60 to win for trainer Charles Lopresti and jockey John Velazquez, who earned his 12th Breeders' Cup victory.
Animal Kingdom, last year's Kentucky Derby winner who had been off for 259 days after his second and most recent injury, finished second.