Chen, the first American men's world champion since 2009, overcame a fall on his quad Lutz in Friday's free skate, but still took the top spot with a combined score of 282.42.
Americans Madison Hubbell and Zachary Donohue had the top score in the rhythm dance, posting a career-best score of 80.53.
During Thursday's short program, the 19-year-old Chen made a mistake on his quad toe loop-triple toe loop combination. He also had a misstep Friday
"I definitely did not do my greatest programs, both short and long," Chen said. "There were mistakes here and there."
He won't have much time to celebrate his win or dwell on his mistakes.
"It's basically right back to (school)," the Yale freshman said. "As soon as I get back from this, I have like a day before my Spanish oral."
Japan's Shoma Uno finished second with 275.10 points.
"It wasn't really a good performance today," Uno said through a translator. "I wish I could have done better."
Junhwan Cha, of South Korea, took bronze with 263.49 in his first appearance at the final.
The 17-year-old trains with Canadian skating legend Brian Orser in Toronto and said he was happy with how he performed in Vancouver.
Friday also saw ice dancers compete in the rhythm dance and pairs skaters performed their short programs.
In the rhythm dance, it was Hubbell and Donohue's first performance since they captured gold at Skate Canada at the end of October, and they've since changed up their program.
"We knew that we wanted a little bit more drama. ... We wanted that roaring finish," Hubbell said, adding that they went into the rhythm dance wanting to "perform fearlessly."
Charlene Guignard and Marco Fabbri of Italy were second with 78.30, while Russians Victoria Sinitsina and Nikita Katsalapov were third with 77.33 points.
Donohue and Hubbell weren't taking their lead for granted.
"Two points is hard to come by and yet easy to lose," Hubbell said. "Certainly our goal stays the same tomorrow, just to make sure we're giving 100 per cent into the performance of this new program, to really make sure we don't get afraid of having something to lose. Because we don't."
The Americans have yet to medal at a Grand Prix Final.
In the pairs competition, Cheng Peng and Yang Jin of China led with 75.69 points after Friday's short program.
"Every move, we did it. So we're happy," Jin said.
Russians Natalia Zabiiako and Alexander Enbert sat in second a score of 75.18 while their teammates Evgenia Tarasova and Vladimir Morozov held third with 74.04 points.
The Grand Prix Final continues Saturday with free skates in the women's, ice dance and pairs competitions.
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