Having opened with a triple Salchow, the 17-year-old could only single the triple Axel that followed but quickly recovered to hit a triple Axel-double toeloop combination, six triple jumps and level-four spins and footwork to impress the judges.
Kihira was awarded 151.16 points for the routine titled "International Angel of Peace," taking her overall tally to 232.34 points after she earned 81.18 points in the short programme segment on Thursday.
"My goal was to get the first place twice in a row... so I became a little bit impatient because of my first mistake in the Axel. But I was able to recalculate and reassemble the structure of my performance," Kihira said.
"I tried to switch my mind and focus on the next element right away after my mistake. It was good experience for me to prepare for the next competition."
It was the fifth straight year that a Japanese woman has topped the podium in the championship, following Kaori Sakamoto (2018), Mai Mihara (2017) and Satoko Miyahara (2016).
Local hope Young You took the silver with a personal best score of 149.68 points to collect 223.23 points overall after a near flawless performance skating to "Evita" where she reeled off a triple Axel and six clean triples.
It was a first ISU Championship medal for a Korean skater since Yuna Kim won gold seven years ago.
American Bradie Tennell claimed bronze for her first medal at an ISU Championship with an overall score of 222.97 points.
In the pairs event, China's Wenjing Sui and Cong Han skated to their sixth Four Continents title. (Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Ken Ferris)