Argentine del Potro, 25, prevailed in both the tie-breakers to beat sixth seed Almagro under a closed roof at the Ariake Coliseum in Tokyo in the second semi-final.
Raonic, who won his second title of the year at last week's Thailand Open, has neither dropped a set nor has been broken in his four matches in the tournament.
Raonic, 22, has won the only meeting against world number seven del Potro in straight sets in Montreal this August.
"In the final, anything can happen," del Potro was quoted as saying by Japan's Kyodo news agency.
"Milos is playing really well. He already won the tournament last week, beating (Tomas) Berdych in the final, and he's here in another final of a big tournament.
"I know his game, and it's tough to break his serve. But as I said, anything can happen in the final and maybe I need to play better than today for me to have a chance."
The Montenegro-born Raonic, who won his first 2013 title after retaining his San Jose crown in February, served 12 aces in the semi-final to boost his four-match tally to 64.
"For me, it's going to be about taking care of my serve primarily, and after that, trying to dictate and play on my terms as much as possible," Raonic said.
(Reporting by Sudipto Ganguly in Mumbai; editing by Amlan Chakraborty)
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