Double Olympic champion Hanyu was favourite to take the men's title setting a national record and claiming victory in the short programme on Friday, but a tired performance in the free skate left the double Olympic champion in second with a total of 282.77 points.
PyeongChang 2018 silver medallist Uno, whose form has been reignited since announcing Stephane Lambiel as his coach, scored 290.57 points to take victory.
16-year-old Yuma Kagiyama claimed third on 257.99 points, Japan's junior champion making the podium in only his second senior nationals.
The podium also confirmed winners of the three places available for the Japanese men's team at the 2020 figure skating Worlds in Montreal next March
Uno's successful defence
Yuzuru hanyu, Yuzuru Hanyu, Yuzuru Hanyu, Yuzuru Hanyu, Shoma Uno, Shoma Uno, Shoma Uno, Shoma Uno.
That's how a list of the last eight winners of the Japan nationals reads, with Uno retaining his place on the summit of Japanese figure skating, Shoma's fourth national title in a row.
Uno landed three quads - hanging on to two of them - in an imperfect display, but this will restore some invaluable self-belief.
New coach bounce
"I’m in the best condition at this point of the season for sure, I was able to skate like myself again," Uno said on Friday after a very impressive short program.
The PyeongChang silver medallist credited his new coach for the change in outlook and energy:
"Stéphane helped me to bring back the joy to my everyday training. I wanted to skate well for him, and go to the battle with him on my team.” - Shoma Uno
Tiredness takes toll on Hanyu
Injuries and illnesses prevented Japan's rockstar skater from competing in the previous three editions of this competition.
And this was Hanyu's third competition this month, the demanding schedule taking its toll on the headline act.
Hanyu stepped out of his opening quad Lutz and only just hung on to a second quad Salchow, the early mistakes draining the energy out of his performance, affecting his customary precision.
Rest and recovery will be top of the list in camp Yuzu with big challenges awaiting in 2020.
The pair will have time to recover and re-focus ahead of the worlds in March, where they'll go head-to-head again.
Hanyu also will be eager to renew his rivalry with reigning world champ Nathan Chen,
The Japanese star called American Chen his 'motivation' after the U.S. skater won their most recent head-to-head at the Grand Prix final thriller in Turin.
Yuma Kagiyama steals show
With all eyes on 15-year-old Shun Sato after he finished third in the short program behind Hanyu and Uno on Friday, it was 16-year-old Yuma Kagiyama who stole the limelight with a stunning free skate on Sunday.
Landing two quads and three triples in a remarkable free skate routine, Kagiyama went from 6th last year to the podium this year in only his second senior nationals, as exciting young world-class skaters continue to roll off the the Japanese production line.
Kagiyama alerted the world to his potential by winning the opening event of this year's figure skating season in Courchevel, France, setting a new junior world record for the combined score along the way.
But his figure skating roots run deep.
Yuma's father is two-time Olympian Masakazu Kagiyama, who coaches his son, and standing on a podium next to reigning Olympic champion Hanyu and PyeongChang silver medallist Uno is a huge breakout moment for junior.
Plenty of positives for Super Sato
Shun Sato may not have landed his first nationals podium but can take heart from his performance, a fall on his opening quad Lutz kept him out of the top three, but his recovery from that first fall was very impressive
Sato illuminated Yoyogi Park landing two of three quads to score 246.50 points overall, and alongside Kagiyama's showing, the future of Japanese figure skating iooks as bright and exciting as its present.
Both Sato and Kagiyama skate with a fluency and maturity beyond their years, Sato expresses himself and interprets the music with an emotion that is incredibly engaging to watch.
Both Yuma and Sato are set to bring much joy to Japan's legion of figure skating fans in the future.
Take a bow Daisuke Takahashi
From junior promises to a senior hero, these national champs were also Daisuke Takahashi's last dance as a singles skater, and he had them wrapped around his finger from the very beginning.
The 33-year-old didn't win, he didn't podium, but it didn't matter.
The love, the applause, the adoration, the standing ovation, Japan's figure skating faithful showed their appreciation for a sparkling career that's lit up three different decades.
They remember the excitement at a rising young star winning the Junior Worlds gold medal in 2002, and when the entire country stopped to watch his Olympic bronze medal win at Vancouver 2010, also when he was crowned World champion in Turin, 2010.
But they remember much more than that - the joy and sacrifice he brought to the sport, the moments of brilliance and beauty that transcended competition.
His smile and sense of humour too - on Friday he said this with a laugh:
"I wish I was ten years younger!" - Daisuke Takahashi
But there's still more to come from one of Japan's favourite ice princes, he'll form a new partnership in ice dance with three-time Japanese champion Kana Muramoto.