The trainer was rewarded when Declan's Moon prevailed by a neck over Roman Ruler on Wednesday, posting a record time in the $250,000 race for 2-year-olds.
Victor Espinoza rode Declan's Moon, who trailed by a half-length into the stretch, over 7 furlongs in 1:21.29 to prevail over a four-horse field in the 57th running of the grade II event.
"I've had a lot of confidence in this horse," said Ellis, whose entry came into the race off a maiden win. "I knew the farther he goes, the better he'll be. He's been training awesome since his maiden win."
Declan's Moon dealt Roman Ruler his first setback in four career races, while breaking the race record of 1:21.60, set by Forest Camp in 1999.
"He was working hard for me, so hard," Espinoza said. "We were in close and side by side through the last part, and my horse was giving me all he had."
Declan's Moon paid $14.40 and $2.10, while Roman Ruler, who went off at odds of 1-10, returned $2.10 to place. There was no show betting because of the limited field, caused by three late scratches.
Chandture, unbeaten in four career starts, was withdrawn on the eve of the race by trainer Bob Hess Jr., who said his horse wouldn't be able to beat Roman Ruler.
"It just goes to show that they can all get beat," said Corey Nakatani, who rode Roman Ruler. "The track was very fast, and you saw how fast they went. (Roman Ruler) laid down his body for me. He tried really hard."
Bob Baffert, Roman Ruler's trainer, was seeking to win for the eighth time in the last nine runnings of the race. He had a string of seven straight victories in this event ended a year ago by Siphonizer, trained by Richard Mandella.
"We're disappointed, but it was a really good horse race," Baffert said. "It was a good time."
Espinoza won this event in 2001 on Officer, trained by Baffert.
Declan's Moon carried 116 pounds, and Roman Ruler ran at the high weight of 120 pounds.
Roman Ruler, who broke slowly, finished 9 1/2 lengths ahead of Swiss Lad. In his previous race, Roman Ruler won the Best Pal Stakes at Del Mar Aug. 15 by 7 lengths over 6 1/2 furlongs.
Maidens Allright and Notarized were scratched on the day of the race.
Ellis won for the first time in this event and claimed his 12th stakes win at Del Mar overall.
Declan's Moon, owned by Mace Siegel and his daughter, Samantha, was purchased as a yearling for $125,000. The race, worth $150,000 to the winner, highlighted the closing day of a 43-day meeting.