Czisny, who won this year's Skate Canada, performed a graceful triple lutz, double toeloop opener followed by a powerful triple flip, double toeloop to George Winston's "Winter and Spring".
She finished third in the free skate with 116.99 points, giving her a total of 180.75.
Czisny had taken the lead Friday with 63.76 points in the short program despite an off-balance trip flip.
"I was very happy to be able to stay on my feet today and very happy with my performance," Czisny said. "Last year, being in this spot was only something I could dream of, but I'm glad I got here and my dream came true."
Despite a left knee injury, Carolina Kostner of Italy was second with a season's best 116.47 in her free skate, giving her a total of 178.60. Kanako Murakami of Japan was a close third with 178.59 in her first senior Grand Prix final since moving up from juniors.
Patrick Chan Wins Gold
Canadian Patrick Chan won gold at the men's free skate program taking advantage of a fall by short program favorite Nobunari Oda of Japan.
The world silver medalist opened with a solid quad toeloop, earning 174.16 points in the free skate and giving him 259.75 overall.
"It's been a dream for me to do well here," the 19-year-old Chan said. "I'm very happy to be able to skate well here, leading up to (the) worlds. It's a very big step for me."
Oda won silver with 156.22 points in his free skate, which was marred by a fall during his opening quad toeloop, for a total of 242.81.
"I was very disappointed with tonight's performance because I fell," Oda said. "I wasn't satisfied with the performance ... I couldn't do the last part because I was so late on the music."
Japan's Takahiko Kozuka came in third with 159.89 in his free skate and a total of 237.79.
Patrick Chan Wins Gold
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