Racing against her favorite rival in Arizona grad Georganne Moline, Carter went 53.84, the fastest time run by an American this year and No. 2 in the world. She edged Moline by .16 seconds.
Moline, who went 54.00, held the fastest time in the country entering Sunday's final and would have lowered her mark had it not been for Carter.
"I got a little shady over hurdles five, six and seven but with eight to go I just decided to go for it and got into Kori-Monster mode," Carter said. "I gave it everything I had, and luckily today it was good enough. It was awesome. I feel so humble, so excited.
"My family is here so it was awesome; it was amazing. Some of the football guys from Stanford are here . . . I have a great support group."
Carter, a nine-time All-American with the Cardinal, was unable to compete in the semifinals of last year's USA Outdoor Track and Field Championships in Des Moines, Iowa because of an intestinal virus.
Carter won the NCAA title in the 400 hurdles last year with a 53.21, the fastest time in the world. She also finished second in the 100 hurdles. She then signed with Nike agent Wes Felix at last year's USATF Outdoor Championships, giving up her final year at Stanford before she was sidelined by illness.
Carter left the program with 11 school records and three Pac-12 titles to go with her All-American status. She turned 22 earlier this month.
Carter reached the finals by running 55.66 in the semifinals. She was second in her heat. In the first round, she clocked 56.26 for the third-fastest time overall.
She now trails only Jamaica's Kalise Spencer in the world rankings. Spencer ran 53.41 in Kingston (Jamaica) just two days before Carter won her title.
Elsewhere on the final day Sunday, Stanford sophomore Valarie Allman placed 12th in the discus throw with a best of 170-1, more than 17 feet off her personal best of 187-7 that set a Stanford freshman record this season.
Allman recorded two throws of 170-1 and fouled in each of her other attempts. She finished second in each the Pac-12 championships and NCAA West Prelims and was 21st at the NCAA championships.
Allman was the national high school leader in the discus with a best of 184-2 at the Texas Relays in 2013, where she set the meet record by 34 feet.
On Saturday, Stanford grad Garrett Heath, also a nine-time All-American with the Cardinal, finished ninth in the men's 1,500 race in 3:40.28. Leo Manzano won the race in 3:38.63.
Heath was the national runner-up in the 1,500 in 2009, a year after reaching the semifinals of the 2008 Olympic trials. He was also a member of the NCAA champion distance medley relay in 2007.
On Friday, Cardinal senior Aisling Cuffe ran 15:13.15 to finish fourth in the women's 5,000 meters. Molly Huddle won the race in 15:01.56. Stanford grad Jessica Tonn was ninth in 15:48.31.
In the men's 5,000, Stanford grad Brendan Gregg was 13th in 13:56.18, while recent grad Erik Olson did not finish the race.
On the first full day of the meet, Stanford grad Chris Derrick finished second in the 10,000 meters in 28:18.18 and Heath qualified in the 1,500 meters by finishing 13th overall.
"I wanted to try to run hard at the front; that's something I need to practice," Derrick said. "I think I did okay. I kind of took stock of the situation with about six to go. I figured he (winner Galen Rupp) might sit on that and kick. I got heavy and for about 30 meters I tried to hold him off as he was preparing to pass and it was over pretty quick. I tried to get my legs moving, they were just a little dead."
Stanford grads Brendan Gregg finished seventh and Jacob Riley was ninth in the 10,000 meters.
Two current Stanford athletes, each a 2014 NCAA outdoor finalist, competed on Thursday: junior Luke Lefebure in the men's 800 and senior Michael Atchoo in the men's 1,500.
Lefebure ran 1:48.37, his second-fastest ever, to finish sixth in his heat and 15th overall, 0.35 from the final qualifying spot on time. Atchoo ran 3:48.47 to finish 12th in his heat and 24th overall.
In the finals of the muli-events at the U.S. Junior Championships, also held at Hornet Stadium, Stanford-bound Harrison Williams won the decathlon title by scoring the second-highest total in U.S. juniors history.
Williams, who signed a national letter of intent with Stanford in February, scored 7,734 points and qualified for the IAAF World Junior Championships on July 22-27 in Eugene, Ore., by finishing among the top two.
"It's very motivating going into world junior," Williams said. "Last year was a little bit of a disappointment. I only got third at youth trials and that gave me a lot of motivation to come back and get a spot on the team."
The score for the Memphis, Tenn., native was second only to the 7,748 by Gunnar Nixon of Santa Fe High (Edmond, Okla.) in 2011 on the U.S. list for those 19 and under.
"My highlights were definitely the long jump, where I PR'ed by a foot, and the 400, where I PRed by more than a second," Williams said.
The heptathlon and decathlon were the only junior championship events being contested in conjunction with the senior meet.
Williams, a recent graduate of Memphis University School, shattered his previous best of 7,181 set in the USA Junior Olympic championships last year. He beat runner-up Gabriel Moore, who is headed to Arkansas, by 140 points. Williams' won only one event, his specialty, the pole vault (16-0 3/4). However, he was second in the long jump, high jump, and 400.
Next up on the track and field schedule will be the 2014 USATF Junior Outdoor Championships at historic Hayward Field on the University of Oregon campus. The meet runs Saturday and Sunday with the top finishers advancing to the IAAF World Junior Championships at the same site in two weeks.
At the USATF Youth Outdoor Championships in Bloomington, Ind., incoming Stanford freshman Lena Giger of Highland, Ill., set a national youth record in the women's hammer with a throw of 183-1. She defeated her closest opponent by an almost unimaginable mark of 30 feet.
At the annual Golden West Invitational, held Saturday at Sacramento State following the USATF meet that day, Menlo School senior Paul Touma finished second in the boys' triple jump at 45-6 1/2. Griffin Kraemer of Sacred Heart Prep was ninth at 40-11 3/4.
Ross Corey from Priory was fifth in the boys' 800 in 1:58.23, Pinewood's Nicole Colonna was seventh in the girls' mile in 5:26.05, Jonathan Alee of Palo Alto was ninth in the boys' 200 in 22.47 and Colton Colonna of Pinewood was ninth in the boys' freshman mile in 4:56.35.
This weekend, recent Menlo School grad Maddy Price will compete at the Canadian Junior Championships in Sainte-Therese, Quebec. She needs to finish among the top two in the 200 and 400 meters to qualify for the IAAF World Junior Championships in Oregon.
Price ranks No. 2 in both events for Canadian junior women. Her bests of 23.97 and 53.42 trail only University of Oregon freshman Christian Brennan's 23.61 and 52.81 this season.
Brennan was the silver medalist for Canada at the 2011 World Youth Championships in both the 200 and 400 meters, setting the Canadian youth record in the 400 (52.12). Her Canadian junior record in the 200 meters (23.43) came at the 2011 Canadian Youth Championship, where she won both the 200 and 400 meters.
Price, meanwhile, holds a solid margin over her closest competitors, Leya Buchanan in the 200 (24.01) and Kendra Clark in the 400 (53.92). In addition to her individual events, Price will have a chance to make the 1,600 relay team. Finals for the 400 will be Saturday with the 200 finals on Sunday.