With a typhoon bearing down on the Japanese capital, the fourth-seeded Nishikori won his second straight tournament and the seventh of his career with a hard-fought victory at Ariake Colosseum.
The contest was a contrast in styles, with Raonic relying on his big serve and Nishikori utilizing his speed and mobility to force his opponent into many unforced errors.
Raonic had 22 aces in a match that featured few long rallies, while Nishikori managed just one.
Sunday's match was a replay of the 2012 final when Nishikori beat Raonic in three sets to become the first Japanese man to win the event.
"It was great to win today," said Nishikori. "It was hard to return against him. He was serving really well, with a high percentage and speed."
Nishikori, ranked seventh, has also won titles this season in Memphis, Barcelona and Kuala Lumpur.
After the first set was on serve until the tiebreaker, Nishikori took a 4-2 lead only to see Raonic run off three straight points to go up 5-4. Nishikori took the set on an amazing save of Raonic's serve, followed by a powerful crosscourt forehand.
Raonic had break points in the first and fifth games of the second set, but could not capitalize. He finally broke to lead 4-3 and took the set with on serve with an ace.
The eighth-ranked Raonic saved three break points in the second game of the final set, but was unable to convert when he had one of his own in the seventh.
Nishikori clinched the match by breaking in the 10th game when the Canadian netted a return.
"I thought it was a great match," said Raonic. "We both played at a high level. He has been playing with confidence lately and taking his shots."
Roanic has reached the Japan Open final for the past three years. He lost to Juan Martin Del Potro of Argentina here in 2013.
"It's disappointing to lose again in the final," noted Raonic. "The last two years have been more disappointing than the first one against Kei." Nishikori is now a strong chance of becoming the first Asian man to qualify for the season-ending ATP World Tour Finals in London in November. The London event features the top eight-ranked players in the world. Nishikori is currently fifth in the standings.
Raonic Question: How high can he go?
The 23-year-old Raonic has one of the game's foremost serves and has steadily risen through the ranks since winning ATP Newcomer of the Year in 2011 at the age of 20.
He works hard, isn't afraid to revamp his game as evidenced by his coaching switch to Ivan Ljubicic and Ricardo Priati as he searches for a more well-rounded game that goes well beyond his 200-kph-plus serve.
But can he go beyond his all-time best ranking of world number 6? Will he ever reach the Big Four of Novak Djokovic, Rafael Nadal, Roger Federer and Andy Murray? Have your say below.