Duhamel, from Lively, Ont,. and Radford, from Balmertown, Ont., weren't pleased with their score of 199.18 points, but it was enough to top teammates Kirsten Moore-Towers and Dylan Moscovitch.
They became the first Canadians to claim this title since Jamie Sale and David Pelletier in 2002.
"We are disappointed," Duhamel said. "We know we are capable of skating much better. We want to show an improved long program at the world championships. We felt confident going in but once the music started it just became a struggle."
Duhamel and Radford, who skated to "Angel," had to fight for their landings on their side-by-side triple Lutzes.
Moore-Towers, from St. Catharines, Ont., and Moscovitch, from Waterloo, Ont., scored 196.78 They won Sunday's free skate but couldn't overtake Duhamel and Radford, who built up a lead in winning the short program.
"We are improving each time out and that's what's motivating us," Moore-Towers said.
U.S. champions Marissa Castelli and Simon Shnapir were third with 170.10 points.
Canada's two-time world ice dance champions Tessa Virtue and Scott Moir lost to American rivals Meryl Davis and Charlie White for the second consecutive competition.
Virtue and Moir had a strong start to their sizzling "Carmen" program, but had to stop about three minutes in when Virtue felt a cramp in her leg. The Canadians were able to resume a couple of minutes later.
"I just had some cramp in my legs to deal with. I'm glad we collected ourselves and kept pushing through the program," Virtue said.
Davis and White scored 187.36. Virtue, from London, Ont., and Moir, from Ilderton, Ont., leaders after the short dance, scored 184.32.
"Tessa and I feel like as a team we have a lot of positive things this week, especially in our short dance," Moir said. "In the free dance, we were able to execute a lot of the elements that we've been struggling with in practice and a little bit at the national championships. Obviously there are a couple of things we want to work on going into the world championships."
Madison Chock and Evan Bates of the United States were third with 160.42 points.
Piper Gilles of Toronto and Paul Poirier of Unionville, Ont., were fifth while Nicole Orford of Burnaby, B.C., and Thomas Williams of Okotoks, Alta., finished sixth.
Two-time world champion Mao Asada won the women's singles title, leading a Japanese sweep of the podium.
After re-introducing her trademark triple Axel in Saturday's short program, Asada was downgraded on the jump in Sunday's free skate but was solid in her other elements to finish with 205.45 points. Akiko Suzuki was second with 190.08 points while Kanako Murakami finished third with 181.03.
"The short program exceeded expectations and the free met my expectations," said Asada, who skated to Tchaikovsky's Swan Lake. "I am happy I was able to challenge the triple Axel and that has given me confidence."
Asada had been struggling with the triple Axel since the Vancouver Olympics but was able to win four events this season without it. She pulled it off to perfection on Saturday when she finished first in the short program. Despite being downgraded on the jump Sunday, Asada said she plans to attempt it at the world championships in London, Ont., next month.
"I plan to include it at the worlds and hope to build on the success I've had here," Asada said.
Canadian champion Kaetlyn Osmond of Marystown, N.L., was seventh, Amelie Lacoste of Delson, Que., finished ninth, while Julianne Seguin of Longueuil, Que., was 11th.
"It was definitely a great experience here and I learned a lot from this competition," said the 17-year-old Osmond. "There were a couple of mistakes but for me it was still a great preparation for the world championships."
The Four Continents is the last major event before the March 11-17 worlds where Asada will renew her rivalry with South Korean skater Kim Yu-na.
Suzuki, who was second after the short program, turned in a strong performance to music from Cirque du Soleil. She under-rotated a double Axel on her second element and was deducted points on a triple Lutz but was solid otherwise to hold on to second place ahead of Murakami, who won her first medal at a senior international Skating Union event.
Murakami was downgraded on a triple flip earlier in her routine but had no major mistakes in the free skate.
"I missed out on a podium at last year's Four Continents because of a poor free skate so I was thinking about that today," Murakami said. "It's great to see a Japanese sweep of the podium.
Christina Gao of the United States finished fourth while China's Li Zijun was fifth.