Baker also took possession of the American record, bettering the time of 58.33 set by Missy Franklin in 2012. Franklin didn't enter the backstroke events at nationals after having surgery on both shoulders 1 1/2 years ago.
Olivia Smoliga was second in 58.75 and 16-year-old Regan Smith took third in 58.83, a junior world record.
Baker completed a sweep of the backstroke events in Irvine, having tied Smith for the 200 title.
"It's really special to be able to have a tie when we both do so amazing," Baker said, "but of course I'm overjoyed with the world record and a first-place swim."
As a result, Baker and Smith earned spots on the U.S. team for next month's Pan Pacific championships in Japan and next year's world championships.
Baker earned a silver medal at the 2016 Rio de Janeiro Olympics in the 100 back.
Baker has been diagnosed with Crohn's disease, which causes inflammation of the digestive tract that can lead to abdominal pain, severe diarrhea, fatigue and weight loss.
Katie Ledecky dominated the 400 freestyle, leading all the way to win by 3.12 seconds for her third victory of the meet.
She earned her 16th national long-course title, tying Natalie Coughlin for seventh on the career list.
Of course, Ledecky has a long way to go to equal or exceed Michael Phelps' record 61 national titles.
"That's super impressive," she said. "I'll have to keep swimming for like 20 years to be able to match that."
Ledecky was under world-record pace through 250 meters with the crowd cheering loudly before she dropped off and finished in 3 minutes, 59.09 seconds. It was the 10th-fastest swim ever in the event, with Ledecky owning the other nine best times.
Baker was warming up when Ledecky was swimming her race.
"I said, 'Kathleen, I think what the crowd needs tonight is a world record,' and she said, 'Yeah,'" her coach David Marsh said.
Olympian Leah Smith gave chase the entire race and touched second in 4:02.21. Another Olympian, Haley Anderson, was third.
Ledecky also won the 200 and 800 freestyles.
Michael Andrew, who turned pro five years ago at 14, won the 100 breaststroke. He rallied from fourth to first in 59.38 seconds, beating a field that included three Olympians.
"Now I've got a spot for Pan Pacs and I've sealed the deal for worlds," he said. "I know there's certain things I can still improve on to get faster and I'm ready to do it."
The men's 100 back was a duel of current and former Olympic champions. Ryan Murphy, who swept the backstroke events in Rio, edged 2012 Olympic winner Matt Grevers, who at 33 is 10 years older.
Murphy touched in 52.51 and Grevers in 52.55.
Olympic champion Lilly King won the women's 100 breast in 1:05.36. Zane Grothe won the men's 400 free.
- AP
