The two-time reigning world champion came from a game down to beat Tsuneyama Kanta as Okuhara Nozomi edged out Yamaguchi Akane.
The two-time reigning world champion admitted he was "too cautious" at the start of his final against world no.11 Tsuneyama Kanta, but came from behind to win 18-21, 21-12, 21-17.
Momota told AFP afterwards, "In the second and third games, I wanted to put all my feeling into it regardless of technique or tactics, and I think I willed myself to the win.
"The Thailand Open starts in the New Year and I'll be able to play against players from overseas. I want to go there and show what I can do as the top Japanese player.
"I'm 70 per cent relieved and 30 per cent happy. I'm known as world No. 1 Momota, so I feel that I'm not allowed to lose." - Momota Kento to AFP
Back in January, hours after winning the Malaysia Masters, Momota was on his way back to Kuala Lumpur International Airport when his car slammed into the back of a truck.
He escaped with minor injuries while the driver of his vehicle was killed.
After returning to training, the left-hander found he had double vision and required surgery repair a fractured eye socket.
The COVID pandemic saw the badminton tour wiped out after March's All England Open giving Momota time to regain full fitness.
The 26-year-old told Olympic Channel recently that he felt no ill-effects following the accident, and he showed that in Tokyo.
He faced his toughest test in the final against Tsuneyama whose biggest win came in the 2018 Thailand Open.
Tsuneyama last beat Momota in the 2017 Canada Open, and took his compatriot to 16-16 in the final game.
But his form deserted him at the vital moment as Momota won four of the last five points to take victory.
The champion admitted, "This week, I hadn't played for a long time so I was very anxious going into each match. But I think my game will start to return now that I've won this title."
Two genuine contenders for gold at Tokyo 2020 met in the women's final with defending champion Okuhara Nozomi just coming out on top.
Like Momota, the Rio 2016 bronze medallist had to come from a game down as she beat world number three Yamaguchi Akane 17-21, 21-14, 22-20.
Okuhara told Kyodo News, "It's always a high-level and intense match when I face Akane and I really enjoyed playing her. I've been working on my footwork during the pandemic and that showed in reacting to her tricky returns."
It was a fourth national title in total for Okuhara who beat reigning Olympic champion Carolina Marin in the final of the Denmark Open, the only international tournament to be held since the BWF Tour was interrupted by the COVID pandemic.
In the women's doubles final, Fukushima Yuki and Hirota Sayaka claimed a third title with a 21-17, 21-12 victory over Matsumoto Mayu and Nagahara Wakana.
Endo Hiroyuki and Watanabe Yuta retained their men's doubles title, beating Hoki Takuro and Kobayashi Yugo 21-19, 21-9.
Watanabe was also successful in the mixed doubles, teaming up with Higashino Arisa to defeat Matsutomo Misaki and Kaneko Yuki 21-11, 21-9 in the final.
Matsutomo won Japan's first ever Olympic badminton gold in the Rio 2016 women's doubles with the now-retired Takahashi Ayaka.