Del Porto, the tournament's No. 1 seed, had the only break of the match late in the second set to claim his third title of this year and 16th overall. Raonic, finishing second at the Japan Open for the second straight year, fell to 5-5 in ATP title matches. He dropped the 2012 Japan Open final to Kei Nishikori in three sets.
Raonic lost only six points on serve in the first set and had chances to grab the lead as del Potro saved three break points and slipped behind 0-2 in the tiebreaker. But del Potro rallied to take the set.
Although Raonic was generally in control on serve -- he won 78 percent of the points when serving -- del Potro took a 0-40 lead in the second set's 11th game. Raonic saved one break point but del Potro won the next and then held serve for the win.
There were only six break opportunities in total for the players, who both won 77 points in the extremely tight match.
The win and 500 rankings points solidifies del Potro's chances of qualifying for the ATP World Tour Finals. He's currently fifth in the race in which the top eight players receive invitations.
The first-place check at Tokyo was worth $312,000 and gives del Potro a career total of more than $13.5 million. Raonic, who is 2-2 in ATP finals this year, picked up $140,700 for second place, giving him career winnings of about $3.4 million.