The highly anticipated Classic was strictly a two-horse race to the finish in front of 55,123.
Game On Dude, the 7-5 favorite, ran what Baffert said was "probably the worst race of his life" in finishing seventh. He lost in the closing strides a year ago at Churchill Downs.
Mott's trio of Flat Out (third), Ron the Greek (fourth) and To Honor and Serve (10th) came up short.
"I don't think we have any huge excuse," he said.
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.
After Tony Bennett sang "The Best Is Yet to Come" as the horses were led onto the track, the spotlight belonged to an unheralded entry 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, the leading rider this year at Ellis Park and Kentucky Downs.
Fort Larned ran 1¼ miles in 2:00.11 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.
"I knew we were good when he broke sharp," Wilkes said. "That's where Brian won the race. We broke sharp and Game On Dude broke bad."
Fort Larned went right to the lead and had things under control, with only Mucho Macho Man picking up the chase. Those two pulled away from the pack with Fort Larned digging in under Hernandez's left-handed whip through the stretch.
Fort Larned's biggest previous win came in the Whitney at Saratoga in August. The colt finished third behind winner Flat Out in the Jockey Club Gold Cup in September.
"No one, I don't think, was too worried about us coming off our last race," Wilkes said. "We could do what we wanted to do and without having that bull's eye."
All the week's attention had focused on Baffert and Mott, two veterans well acquainted with winning on the big days.
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.
"It was a tough day for me, but I've had tougher," the white-haired trainer said. "Joe Torre told me that you've got to forget it."
Torre, the retired manager of the Los Angeles Dodgers and New York Yankees, co-owns Game On Dude, who could never employ his favored front-running style under Rafael Bejarano.
"At the three-eighths (pole) he gave me his move," the jockey said. "And then, all of a sudden, he was flat, totally out of gas. I can't understand it and I can't explain it."
Mott was trying to duplicate his feat from last year when he won the Ladies' Classic and the Classic with Drosselmeyer.
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.
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 set 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.
Wise Dan, the 9-5 favorite in the $2 million Mile, came through with a 1½-length victory, covering the distance in a track-record 1:31.78. He paid $5.60 to win under jockey John Velazquez, who earned his 12th BC 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.
The string of upsets continued with Little Mike winning the Turf by a half-length under jockey Ramon Dominguez. He paid $36.60, the highest win price for this year's event.
The win price on Little Mike topped Calidoscopio's payout of $36.40 in the $500,000 Marathon on Friday.
Tapizar beat a talented field that included 5-2 favorite Emcee and Shackleford. He won by 2¼ lengths and paid $32.60 for trainer Steve Asmussen.
Trinniberg won the $1.5 million Sprint by three-quarters of a length at 13-1 odds, triggering a win price of $29.40. Defending champion Amazombie, the 7-2 favorite, was eighth.
Baffert, a three-time Sprint winner, got shut out with his entries of Fast Bullet (sixth), Coil (seventh), Capital Account (12th).
In the $1 million Juvenile Turf, 9-1 shot George Vancouver won by 1¼ lengths and paid $20.60. Trainer Aidan O'Brien, jockey Ryan Moore and owner Coolmore Stud teamed to win for the second straight year.
Filly Mizdirection beat the boys by a half-length in the $1 million Turf Sprint off a six-month layoff, giving sports talk radio host and co-owner Jim Rome his first Breeders' Cup victory.
"I'm numb," he said. "Having a hard time believing that that happened."
Sent off at 6-1 odds, Mizdirection paid $15.80, $7.40 and $5. Hall of Famer Mike Smith won his 17th Breeders' Cup race and second of the weekend, extending his record for wins among jockeys.
Groupie Doll came through as the 3-5 favorite in the $1 million Filly & Mare Sprint, winning by 4½ lengths. Jockey Rajiv Maragh won his second race of the weekend, having taken the $500,000 Juvenile Sprint on 15-1 shot Hightail on Friday.
In the Juvenile, Shanghai Bobby ran 1 1/16 miles in 1:44.58 and paid $4.60, $3.40 and $2.60. He's Had Enough returned $12.60 and $7.40 for trainer Doug O'Neill, jockey Mario Gutierrez and owner J. Paul Reddam, the same connections behind Kentucky Derby and Preakness winner I'll Have Another.
Capo Bastone paid $5 to show.
Baffert's duo of Power Broker and Title Contender finished fifth and eighth, respectively.