Nadal broke Soeda with a perfect lob to close out the first set and wrapped up the victory in 1 hour, 30 minutes at Ariake Colosseum.
"I'm really happy with my serve," Nadal said. "The ball was a bit heavy. It was difficult for my topspin."
The 10-time Grand Slam champion, who got in 85 percent of his first serves, will play Milos Raonic of Canada in the second round. Raonic beat Japanese wild card Yuichi Sugita 6-7 (4), 6-3, 7-6 (1) to advance.
"(Raonic) is a dangerous player for me in the second round," Nadal said. "He has one of the biggest serves on the tour."
Third-seeded David Ferrer of Spain ousted Kei Nishikori of Japan 6-4, 6-3 in another first-round match. The fifth-ranked Ferrer saved two break points in the final game of the second set, before converting his first match point.
He also saved two break points at 2-2 in the second set before breaking in the next game with a crosscourt forehand winner.
Ivan Dodig of Croatia also advanced by ousting eighth-seeded Juan Monaco of Argentina 6-3, 2-6, 7-6 (1). Dodig saved a match point in his final service game of the third set before dominating the tiebreaker.