Djokovic, who is attempting to win a title on his tournament debut for the 10th time, hit 10 aces and saved three of four break points.
Djokovic retired with a left-shoulder injury during his fourth-round match against Stan Wawrinka at the U.S. Open but showed no lingering effects in Tokyo.
With Djokovic serving for the win, Soeda broke his opponent for the first time when Djokovic double-faulted to make it 5-4. But the top-ranked Serb broke Soeda for the fourth time in the final game.
Djokovic, who is 42-8 this season with three titles in four finals, will next face either Yoshihito Nishioka and Lucas Pouille.
Also, Yasutaka Uchiyama beat Radu Albot 6-7 (2), 6-3, 6-4, and third-seeded David Goffin rallied to beat Pablo Carreno 1-6, 7-6 (8), 6-0.
Goffin is the lone former champion in the draw. He has made the final in both of his previous appearances, falling to Nick Kyrgios in the 2016 final before defeating Adrian Mannarino for the title in 2017.
More AP Tennis: https://www.apnews.com/apf-Tennis and https://twitter.com/AP—Sports