Baffert, who was "horseless" just three weeks ago, was lucky enough to have War Emblem land in his training barn after Saudi Prince Ahmed Salman bought him after the son of Our Emblem won the Illinois Derby.
The win was Baffert's third in the last six Derbys. The white-haired trainer won with Silver Charm in 1997 and Real Quiet in 1998.
War Emblem, as expected, set the pace in the 1¼-mile Derby, and never let go of the lead. He became the first Derby winner to lead from the start since the filly Winning Colors in 1988.
Ridden by Victor Espinoza, War Emblem won by four lengths over Proud Citizen, trained by D. Wayne Lukas, with Perfect Drift three-quarters of a length back in third. Medaglia d'Oro was fourth.
The win was a sweet one for Baffert, who was denied a Derby win last year with the favored Point Given, who went on to take the Preakness and Belmont Stakes.
Espinoza, a first-time Derby winner, said he knew he had the race won at the half-mile pole.
"He was going so easy. I knew nobody was going to catch me," he said.
Despite the late scratches of Wood Memorial winner Buddha and Baffert's long shot Danthebluegrassman, the field of 18 3-year-olds was one of the most wide open in years.
With no designated super horse like Point Given or Fusaichi Pegasus two years ago to grab the bettor's fancy, Harlan's Holiday and Saarland went off at co-favorites at 6-1 - the highest odds ever for Derby favorites.
Unlike other Derbys, there was little backstretch buzz during the week, with enough storylines to keep crowds around the barns to a minimum. Not even Baffert or Lukas drew their usual large audiences.
Security was apparent at almost every turn Saturday, with National Guardsmen and police weaving in and out of crowds of racing revelers.
On a sunny and breezy day at Churchill Downs, a crowd of 145,033 came to wager in one of the best betting Derbys in years. The crowd was the fifth largest in Derby history.
Heightened security has become a fact of life at major sports events since the Sept. 11 terrorist attacks, and the Derby was no different. Six New York City firefighters were honored before the race.
War Emblem, who won his fifth race in seven career starts, covered the distance in a speedy 2:01 - seventh-fastest in Derby history. The record belongs to Secretariat at 1:59 2-5 in 1973.
The colt returned $43, $22.80 and $13.60. Proud Citizen, who earned his spot by winning the Lexington Stakes, paid $24.60 and $13.40. Perfect Drift paid $13.40 to show.
During the week, Baffert said all he could do is train War Emblem aggressively and hope the front-runner could hold off the competition.
"If this horse wins the Derby, it will be the best and shortest training job ever," Baffert said before the race.
Request for Parole was fifth, followed by Came Home, Harlan's Holiday, Johannesburg, Essence of Dubai, Saarland, Blue Burner, Castle Gandolfo, Easy Grades, Private Emblem, Lusty Latin, It'sallinthechase, Ocean Sound and Wild Horses.