Olympic silver medallist Uno completes Japanese double after Rika Kihira came from fifth to first in the ladies' singles in Anaheim.
Shoma Uno produced a world record free skate to take the Four Continents title in Anaheim.
Coming into the competition with an ankle injury, the Olympic silver medallist was below his best as he took fourth in the short program.
But the Japanese Olympic silver medallist decided not to alter his free skate, landing three quads in a near-flawless routine to clinch the biggest win of his career.
Defending champion Jin Boyang was second ahead of home skater Vincent Zhou who led after the short program.
What made Uno's achievement all the more impressive is that he has been suffering with a right ankle injury since winning his third consecutive Japanese national title in December.
After practice on Wednesday, he said he initially took 10 days off but had to take another break after spraining it again.
He then tweaked it for a third time in late January and barely trained before this competition in California.
But after his free skate, Uno fell to his knees in elation.
"It was like 'Oh, I really did it.' - Shoma Uno after his winning free skate
"I thought about how I was injured after Nationals and how I can bring my skating to the next level. I think I was able to do everything I can."
Skating to Beethoven's Moonlight Sonata, Uno started with a quad flip and a quad toe loop.
He later landed a quad toe loop into double toe loop combination to break Hanyu's world record.
Uno then had to wait 40 minutes for the remaining skaters to go before being confirmed the winner.
Now he has five weeks to rest and prepare for the World Championships on home ice in Saitama where double Olympic champion Hanyu and defending world champion Nathan Chen are likely to be the favourites.
Jin Boyang was second in the free skate to move up a place to second overall.
But the Chinese skater insists there is improvement to come ahead of next month's Worlds.
He said, "I wanted to put on a better performance. My skating wasn’t that relaxed.
"Two minutes before stepping on the ice, I decided to not do the quad Salchow in my program and change some of the choreography."
Vincent Zhou was happier despite slipping from first to third on the free skate after being marked down on three of his jumps.
He said, "I think it’s a good thing that I wasn’t perfect at this competition. Because if I were perfect then I wouldn’t have anywhere to go for worlds."
South Korea's Junhwan Cha was fourth ahead of his training colleague Jason Brown.
Since joining Brian Orser ahead of this season, 2015 American national champion Brown has been working hard on adding quad jumps to his repertoire.
And though he is yet to land a clean quad in competition, he came very close with a quad Salchow on Saturday night.
Brown said, "But I rotated! I know it wasn’t rotated cleanly, but you know what? I did three double sals at the beginning of the season, each competition, so to at least go out there it’s a step forward.
"Every single competition I've gone to, I’ve just gotten stronger and stronger.
"I'm not where I’d like to be in the long run, but that being said I'm just super, super proud of each step that I’m making this season and hopefully continue on making into the next four years."
Rika Kihira is the woman to beat in Saitama after producing another superb free skate.
Just as she did when she made her name in the NHK Trophy, Kihira took victory having been in fifth place after the short program.
The Grand Prix Final winner opened with a triple Axel and landed seven more triples to score 153.14 points and come out on top in an extraordinary competition.
The top three from the short program - Bradie Tennell of the United States, Japan's Kaori Sakamoto and Tennell's team-mate Mariah Bell - all finished off the podium.
Elizabet Tursynbaeva was second to become Kazakhstan's first female ISU Championship medallist with Mai Mihara making it gold and bronze for Japan.
Kihira has struggled with her skating boots all season and arrived in Anaheim with a new boot on her left foot.
She popped a triple Axel in the short program but, after suffering her first defeat of the season at the Japanese nationals, made no mistake in the longer skate.
And the 16-year-old said, "I was able to leave yesterday's mistake behind. During this season, I have learned to keep my concentration in my free skating no matter what happens in my short program."
After five years with Orser in Toronto, Tursynbaeva returned to her birthplace Moscow to train alongside Olympic champion Alina Zagitova under Eteri Tutberidze at the start of this season.
The 18-year-old just failed to land a quad Salchow on her first jump and hopes to nail it in Saitama next month.
She said, "After the short program, being sixth, I had nothing to lose so we decided I had to try the quad Salchow. I'm happy I attempted it and will keep trying until I land it.
"This is unexpected for me. I didn't think I would be on the podium today."