Chan, who was first after the short program on Thursday, started off well with a quad toeloop-triple toeloop combination but things went downhill after that. He fell on the triple Axel, the triple-Lutz-double toeloop and the double Axel.
"It's frustrating to end the season like this," said Chan, who finished second overall. "I don't really have a choice for this competition and did it for the team. I had a good season with the world championships but it's hard to travel all this way, my body is not happy competing at this time of year."
Japan's Daisuke Takahashi finished first overall after topping the free skate with 168.65 points. Kevin Reynolds of Coquitlam, B.C., was second in the free skate with 164.13 to jump from ninth to third place overall.
"I was very relieved the close out the season with a strong performance," Reynolds said. "I was able to fight back and believe in myself and my training."
Max Aaron of the United States was third with 159.24.
Takahashi hit his opening quad and was good enough to lead despite mistakes on three combo jumps.
"I wanted to do the quad without worrying too much about it," Takahashi said. "I wasn't completely satisfied with my routine but was glad I could help my team."
The United States moved into first place in the overall standings thanks to the win by Madison Chock and Evan Bates in the ice dance final. Canada moved from fourth to second while Japan was third heading into the final day of competition.
"I'm so proud of all our team members today," Chan said. "Kevin really made the difference for us and helped us make up ground from day one. Everyone stayed positive and we ended off on a good note."
Chock and Bates won with 164.91 points, followed by Canadians Kaitlyn Weaver and Andrew Poje of Waterloo, Ont., (160.08) and Russians Ksenia Monko and Kirill Khaliavin (149.27).
"It was a good challenge for us to finish the year off strong," said Weaver celebrating her 24th birthday. "After worlds we had to get back into rhythm of competition. We weren't at our best here but it was a great way to cap the season."
Russia's Tatiana Volosozhar and Maxim Trankov led after the pairs short program, Meagan Duhamel of Lively, Ont. and Eric Radford of Balmertown, Ont., were second, and French couple Vanessa James and Morgan Cipres third.
"The way we performed today was beyond our expectations we are so happy to end our La Boheme program with that performance," Radford said.
The World Team Trophy brings together selected skaters from the six countries that scored the highest combined points at major senior and junior competitions. For the first time a team event, which differs slightly to the World Team Trophy format, will be included in next year's Sochi Winter Olympics.
The competition wraps up on Saturday with the pairs and women's free programs. Kaetlyn Osmond of Marystown, N.L., and Gabrielle Daleman of Newmarket, Ont., were seventh and 12th after Thursday’s women's short program.
— With files from The Canadian Press.