Top-seeded Ferrer, looking to bounce back from an opening-round exit in Beijing last week, defeated Levine 6-4, 4-6, 6-1 in his first match of the tournament.
"Every week is different,'' said Ferrer. "I played a very good match today, a lot better than last week.''
Ferrer won the first set with a crosscourt forehand and looked set for an easy win but Levine bounced back, breaking Ferrer in the first game of the second set.
Ferrer took control in the third set, breaking Levine twice before winning with his fifth ace of the match.
Ferrer defeated France's Richard Gasquet in last year's final and relishes the Tokyo tournament.
"It's very special here,'' said Ferrer. "I have a lot of fans here and winning here last year was a great experience for me.''
The Spaniard will meet either No.15 Simone Bolelli of Italy or Japanese wildcard Takao Suzuki in the third round.
In other second-round matches, Germany's No.12 Rainer Schuettler defeated South Korea's Lee Hyung-taik 6-3, 6-7 (3), 6-3. Schuettler will next face either No. 8 Mikhail Youzhny or Italy's Flavio Cipolla.
Austrian No.14 Jurgen Melzer downed Germany's Simon Stadler 6-2, 6-3. His third-round opponent will be the winner of Wednesday's late game between American No. 2 Andy Roddick and will Ivo Minar of the Czech Republic. Roddick had a first-round bye.
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