Tatsuki Machida of Japan took the gold medal with 269.09 points, Jason Brown of the U.S. was second with 234.17, while Nguyen scored 232.24 to finish third.
The 16-year-old from Toronto landed the quad and two triple Axels — including one in combination — in the opening minute of his program to music from "La Strada." He added five more triples including a beautiful Lutz to cap the program.
The medal was a bit of a surprise for Nguyen, who was seventh after the short program on Friday.
"I didn't have a great week of training so it's nice to finish like this with a satisfying performance," said Nguyen who is coached by Brian Orser. ''The start of my program is important but I know I still have the rest of the program to focus on."
Nguyen landed the quad Salchow for the first time last week in a silver medal performance at Skate Canada's Autumn Classic in Barrie, Ont.
"I felt today's jump had a lot more power in it and I'm looking forward to doing it again at my next competition," Nguyen said.
Americans were 1-2 in ice dancing. Madison Chock and Evan Bates won the gold medal with 171.03 points and Maia Shibutani and Alex Shibutani were second with 160.33. Russians Alexandra Stepanova and Ivan Bukin were third at 143.87.
Elisabeth Paradis of Loretteville, Que., and François-Xavier Ouellette of Laval, Que., climbed from eighth after the short dance to fourth at 137.30 in their senior Grand Prix debut. Nicole Orford of Burnaby, B.C., and Thomas Williams of Okotoks, Alta., were eighth.
In pairs after the short program, Vanessa Grenier of Sherbrooke, Que., and Maxime Deschamps of Vaudreuil-Dorion, Que., are sixth.