Miura and Kihara had taken the overnight lead with a personal-best short programme score, and sealed the deal in the free skate to finish ahead of American rivals Alexa Knierim and Brandon Frazier.
The Japanese pair finished with an overall score of 222.16, ahead of Knierim and Frazier on 217.48 and third-place Sara Conti and Niccolo Macii of Italy on 208.08.
"Riku was injured after the Beijing Olympics so we had a difficult season," said Kihara.
"But we have a relationship of trust and our bond pushed us to grow."
Miura and Kihara's win has stoked hopes of a Japanese clean sweep among home fans as the country hosts the world championships for the first time since 2019.
Russian skaters have again been banned from the competition because of the war in Ukraine.
Cheered on by the crowd, Miura and Kihara gave a largely solid performance, although a slip by Miura late in the routine left them sweating on the judges' score.
The pair, who have competed together since 2019, broke down in tears once their victory was confirmed.
"We have some regrets from the free skate but I'm very, very happy," said Miura.
Knierim and Frazier went into the free skate in second place but a wobbly landing on one jump from Knierim gave them too much work to do to catch the leaders.
The American pair had finished second behind Miura and Kihara by just one point at the Grand Prix final in December.
Miura and Kihara also won the Four Continents title in February.