Nishikori dropped the first set and needed courtside treatment on a hip injury ahead of the decider before prevailing 4-6 6-0 7-6(2) in a duel that lasted an hour and 47 minutes.
Becker nearly silenced the 10,000 spectators at the Ariake Colosseum by claiming the first set when Nishikori hit a forehand return into the net.
The local fans soon found their voice, however, when U.S. Open finalist Nishikori bounced back in style, storming through the second set with the concession of just 11 points.
Nishikori raced to a 3-1 lead in the decider but Becker refused to throw in the towel and broke back to eventually force a tie-breaker that his opponent dominated.
"It was a tough match," Nishikori told reporters. "He started really well and I have to give him credit for the first set. I started playing well in the second and it was really tough in the third set.
"In the tie-break, I was able to raise my level and I used my forehand better.
"I experienced nerves so I tried to focus on my first serve, because he was serving bombs. They were tough to return. In the tie-break anything can happen and I got lucky," he added.
ATP FINALS
The victory ensures Nishikori will move up to fifth place in the race for one of the eight spots available at the ATP Finals in London from Nov. 9-16.
Novak Djokovic, Rafa Nadal and Roger Federer have already guaranteed their places at the season-ending tournament.
Sunday's final will be a rematch of their marathon U.S. Open fourth round duel that equalled the record for the latest match ever played at the year's final grand slam.
Nishikori outlasted Raonic 4-6 7-6(4) 6-7(6) 7-5 6-4 in four hours and 19 minutes at the Arthur Ashe Stadium before going on to become the first Asian male to reach a grand slam final.
"It's going to be a tough match," Nishikori said of the final.
"He is playing really well this week. We always battle. It is amazing to play against him in a final here."
Losing finalist in the last two editions of the Tokyo tournament, Raonic stayed on course to be third time lucky with a comprehensive 6-1 6-4 win over Frenchman Gilles Simon in a rain-interrupted match.
"Against Kei, it is something to look forward to," Raonic said looking ahead of the summit clash against the player who beat him in the 2012 final.
"A lot of people here want it. I have to execute well and serve well, focusing on myself primary other than them," said Raonic, who has sent down 900 aces this season.
(Reporting by Amlan Chakraborty; Editing by John O'Brien)
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