Nishikori downed Kendrick 7-6 (3), 6-7 (5), 6-2 at Ariake Colosseum and will meet Spain's Guillermo Garcia-Lopez in the second round on Wednesday.
Defending champion David Ferrer of Spain - the top-seeded player at the US$869,000 (?605,000) tournament - has a first-round bye along with second-seeded Andy Roddick of the United States.
In other first-round matches, Croatia's Roko Karanusic defeated Japanese qualifier Hiroki Kondo 6-2, 6-2. Karanusic will next meet No. 9 Tomas Berdych of the Czech Republic.
Wayne Odesnik of the United States downed compatriot Kevin Kim 6-4, 6-3 to set up a clash with Serb Viktor Troicki, while Jesse Levine, also of the United States, rallied for a 4-6, 6-1, 6-0 win over Thailand's Danai Udomchoke. Levine will face Ferrer in the second round.
In the US$175,000 (?121,000) women's bracket, there were two upsets.
Russian 17-year-old Anastasia Pavlyuchenkova knocked out third-seeded Zheng Jie of China 6-1, 6-2, while Klara Zakopalova of the Czech Republic eliminated fourth-seeded Maria Kirilenko of Russia 4-6, 6-2, 7-5.
Pavlyuchenkova advanced to a second-round meeting with Japanese qualifier Rika Fujiwara, while Zakopalova will take on Poland's Marta Domachowska.
Top-seeded Caroline Wozniacki of Denmark avoided becoming another high-profile casualty when she rallied from a set down to defeat Gisela Dulko of Argentina, 4-6, 6-0, 6-3. Wozniacki's next opponent will be Japanese wildcard Ayumi Morita.
Israel's Shahar Peer, seeded sixth, defeated Japanese veteran Kimiko Krumm Date 6-3, 6-1. The 38-year-old Date, who made her comeback to pro tennis this year, won this tournament four times in the 1990s.
Nishikori took control of his match when he broke Kendrick with a blistering crosscourt forehand to go ahead 3-2 in the third set. He won the match when Kendrick's return in the final game was long.
"He's got a very good serve,'' the 18-year-old Nishikori said of his opponent. "I knew I just had to wait for a chance and finally I got it in the third set and was able to break him.''
Nishikori was returning to Japan after losing in the first round of this tournament in his debut last year.
He beat American James Blake at Delray Beach in February to win his first ATP singles title and also beat World No. 4 Ferrer in the third round of the U.S. Open before falling to Juan Martin del Potro in the fourth round.
Nishikori said his experience in the past year has made him a better player.
"It's a huge relief to win here in Japan,'' said Nishikori, who is 84th in the world rankings. "Last year, I was very nervous and couldn't play my game. This year I was nervous too but was able to settle down and I think that's a result of the confidence I've built up in the last year.''
Nishikori has given the men's game a boost in Japan, which - until his win earlier this year - had not had a winner in men's singles on the ATP tour since Shuzo Matsuoka won in Seoul in 1992.
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