Nadal roared out in the first set, breaking Monfils in the second and sixth games and keeping the Frenchman off the net with deep, well-placed returns that sealed it up in just 25 minutes at 6-1.
Monfils took back some of the momentum early in the second set, delivering strong serves and crosscourt returns -- and pleasing the crowd with acrobatic saves.
But the left-handed Spaniard fought back in the 11th game, breaking Monfils' serve with a long return shot just out of reach that put him ahead 6-5. He then held his serve to take the next game and the match at 7-5.
"I have to enjoy this moment," the 24-year-old Nadal said, promising to return next year. "You never know when it will end."
Nadal, who has won nine career Grand Slam titles and seven of eight finals this season, went into the match a heavy favorite, having beaten Monfils in six of their last seven meetings. His only loss to the Frenchman came on Doha's hard surface last year.
Monfils has also struggled against left-handed opponents, with an 0-3 record against them this season.
"I wanted to win another big title after the U.S. Open," Nadal said. "Every tournament is very important."
But Nadal, fresh off an upset loss in Bangkok to compatriot Guillermo Garcia-Lopez, said going into the match that he was tired from a long season and was having trouble concentrating.
Though he breezed through his early matches in Tokyo, winning in straight sets, that fatigue showed in his semifinal against unseeded Viktor Troicki, who was at match point twice and forced the top-seeded Nadal into two tiebreakers before he finally capitalized on the Serb's sloppy play.
Nadal had only one ace, to nine served up by Monfils, but won 90 percent of points on first serves.
Still, he said he was able to shake off the previous day's doldrums and was satisfied with his performance Sunday.
"Though there was a lot of tension against Troicki, it wasn't physically very demanding," he said, adding that he pushed Monfils hard and saw the win as the product of his own aggressive play rather than Monfils' early mistakes.
"I started playing at high intensity, and that's why I won the match," he said. "I was very comfortable with myself."
Monfils, who is ranked 15th in the world and defeated second-seeded Andy Roddick in a hard-fought match en route to the finals, said he started off slowly because he warmed up with the arena roof closed and could not get used to the sunlight as it opened just before the competition began.
"It was hard for me to adjust my game," he said. "It is hard to beat Rafael outdoors."
He said that although he slipped early in the match, twisting his ankle and bloodying his shin, that was not a factor in his defeat.
"It only affected me for a few seconds," he said. "I think Rafael just played solid. I could not find a solution."