The reigning world champion, who was second after the men's short program, barely made the podium after finishing just 0.04 points ahead of Spain's Javier Fernandez on Saturday.
Japan's Daisuke Takahashi won gold despite falling on his opening quad, while his compatriot Yuzuru Hanyu finished second.
Chan also fell on his initial quad, which was to be a combination with a triple toe-loop.
"To be honest, I'm pretty disappointed with my performance today," said the Toronto native, who was the two-time defending champion at the event. "Looking at the whole program I think there were a lot of good things also — I did the triple axel-triple loop sequence, those two jumps that I missed at Cup of Russia.
"So each competition I'm kind of tuning in onto every little detail of the program, which is what I like to see."
Takahashi recovered from his opening fall to land a quad toe-loop, but made other errors including a hand down on a triple-double. He took gold with mixed emotions.
"Of course I am the champion of the GP Final but there's a lot to be done, there's a lot of challenges and issues that remain," he said.
Chan wasn't the only Canadian going home with a medal and things to work on. World champions Tessa Virtue and Scott Moir settled for silver in ice dancing after losing out to Americans Meryl Davis and Charlie White.
"It was a great skate for us," said Virtue. "We had to fight through it but that's not surprising considering the intensity of the competition. We are where we want to be at this point and we just have to go home and fine tune the program. There's a lot of room to grow."
Virtue, from London, Ont., and Moir, from Ilderton, Ont., both in all black, made a moving interpretation of the classic "Carmen" story.
"It was definitely a program we had to work through, but our execution was spot-on today. We had a really good, strong technical skate and we were able to bring the motion as well. So that's exciting, especially in this venue, to lay down two strong skates," Moir said, referring to the Iceberg arena's future role as host for figure skating at the 2014 Olympics.
Davis and White performed an array of complex moves, including one in which he appears to drop her but holds on with one hand while she wraps her legs around one of his.
Both duos said the ease they showed on the ice was deceptive.
"It was one of those skates when nothing really came easily, we felt like we had to fight through it but that's OK," Davis said. "It's good to have skates like that, and it's really times like that where we feel we grow the most."
Nathalie Pechalat and Fabian Bourzat of France took bronze.
In women's singles, Japan's Mao Asada used a clean free program that ranged from sprightly to quietly refined to win gold ahead of American Ashley Wagner. Japan's Akiko Suzuki was third.
Asada landed six triples in her program to excerpts from Tchaikovsky's "Swan lake," a musical choice that delighted the Russian spectators to boost Asada's spirits.
"When it began, I head some people clapping and I was happy to hear that," she said. "Looking back on my performance there were no major mistakes, so that's a great takeaway from today."
Asada's only significant misstep was doubling what would have been her seventh triple of the program. But her presentation followed the music's emotional range, from the dreamy opening to its lively conclusion.
Wagner, who was just half a point behind Asada heading into the free skate, fell twice and ended up a distant second.
Wagner said her second fall, a frontal plunge on a double axel in combination after a triple loop "was a bit of a freak fall. But to have such a hard fall and then go and complete the triple flip of that quality is definitely something I can take away from this competition."
She'll also take away some pain from the fall. The team doctor told her she injured a hip.
"I can't tell you what that is but I can tell you it really hurts," Wagner said. "For me, I always like to go big or go home, so when I fall I like to fall really hard."
In pairs, Russia's Tatiana Volosozhar and Maxim Trankov won gold. Meagan Duhamel Lively, Ont., and Eric Radford of Balmertown, Ont., finished fourth just ahead of Kirsten Moore-Towers of St. Catharines, Ont., and Dylan Moscovitch of Toronto in fifth.
"That was one of our strongest long programs this year," said Duhamel. "The throws were a lot cleaner, the twist was great and the side-by-side Lutz was good. We took the time to perform the program well. Unfortunately we had one major error that was costly."