The 21-year-old from Toronto was second after Friday's short program, tripling what was a planned quadruple toe loop, then touching a hand down on his triple Axel.
"You know the jumps. . . jumps are jumps," Chan said. "They worked in the six-minute warmup, but it's so different doing it on the ice with five other guys on the six-minute warmup than being all alone on the ice by yourself, it's intimidating. I don't compete just enough to be comfortable with that yet."
Chan scored 82.52 points for his program choreographed by former world champion Jeff Buttle, and set to music by Rachmaninoff.
Javier Fernandez of Spain, who's coached by Canadians Brian Orser and Tracy Wilson, is the leader with 85.87, landing a textbook quad toe loop. Japan's Nobunari Oda is third with 82.14.
Canada's Olympic and world ice dance champions Tessa Virtue and Scott Moir lead by just .01 points after botching a lift in their short dance.
Rising star Kaetlyn Osmond is second after the women's short program, while her Canadian teammates Meagan Duhamel and Eric Radford were second after the pairs short program.
Chan, whose seasons have been known to get off to slow starts, was third after a sloppy short program last year at Skate Canada before roaring back to win the title.
He blamed a lack of speed heading into his quad attempt Friday night, plus some choppy ice around the corners at the Windsor Family Credit Union arena.
"I think (tripling the quad) was less shocking than a fall," he added. "I think it's the first time ever I've popped in my program, it kind of hit me as I was going into the triple Axel. It's a difficult position to do that and then gather yourself to do a triple Axel. These are all things I'm learning.
"Even after four or five years on the circuit, there's still a lot of things to learn."
Chan's program was a noticeable departure from the ones choreographed by Lori Nichol. Chan left Nichol in the off-season to work with Buttle and David Wilson, who choreographs his free program. He also has a new lead coach in dance teacher Kathy Johnson after Christy Krall resigned as his coach the day after the world championships last March.
Chan admitted it took him a while to buy into his new programs, but said he was feeling his short program Friday night.
"It's a very quiet piece, it's very simple, it doesn't have many instruments, it just has a piano, so there's a lot of quiet moments in the music," Chan said. "I think as you get more mature and more experienced as a skater, that's the challenge, to make something beautiful out of nothing. To make something great out of just silence.
"Those little things are what separates you as a skater, and you have to have some kind of confidence and comfort knowing that during those subtle moments you can not make it awkward and make it comfortable. When I'm doing a lot of steps in the program, I have chills through my body."
In ice dance, Virtue, from London, Ont., and Moir, from Ilderton, Ont., scored 65.09 points for their program set to a waltz written by Sir Anthony Hopkins.
Virtue, wearing a gauzy teal dress, and Moir, in a smart blue jacket and slacks, lost major marks for a messy lift — the same one that kept Virtue and Moir out of a competition earlier this month in Finland when Moir injured his neck.
"It just didn't go as well as we'd been practising it," Moir said. "The transition wasn't very smooth and sometimes when you put a lift at two minutes and 45 seconds, that's the risk you take. It hasn't been like that at practice but it is a lift we've been thinking of changing anyways. It'll be interesting to see how much longer that lift lives."
Italy's Anna Cappellini and Luca Lanotte were second with 65.08 points, while Russians Ekaterina Riazanova and Ilia Tkachenko were third with 55.80.
Piper Gilles and Paul Poirier of Unionville, Ont., are fifth, while Toronto's Kharis Ralph and Asher Hill are eighth.
In women's singles, Osmond scored 60.56 points for her performance to Mambo No. 8, a program that included a triple toe loop-triple toe loop combination.
Canada hasn't had a top world-class women's skater since 2010 Olympic bronze medallist Joannie Rochette, and the 16-year-old Osmond, from Marystown, N.L., would like to change that.
She was the surprise winner of the short program at the Canadian championships last winter en route to winning bronze. She captured her first international title at the recent Nebelhorn Trophy in Germany.
"It brought me into the senior groupings and brought my confidence up, and made training that much more enjoyable and much better," she said of her Canadian bronze.
Elene Gedevanishvili of Georgia, who is also coached by Orser, scored 60.80 to sit in first place. Ksenia Makarova of Russia was third with 58.56 points while Amelie Lacoste of Delson, Que., was seventh with 53.81.
Osmond looked perfectly at ease on the ice, and said she doesn't feel any added pressure now that she's in the spotlight.
"I definitely love performing ... when I heard everyone cheering it just took all the nerves away," she said. "When I'm skating, trying to put on a show for everyone else just makes me that much more confident in what I'm doing and that much more enjoyable."
In pairs, Duhamel, from Lively, Ont., and Toronto's Radford scored 64.49 for their skate to "La Boheme."
Four-time world champions Aliona Savchenko and Robin Szolkowy of Germany — dressed in multi-coloured bodysuits and skating to "Kismet" by Bond — scored 72.26. Italians Stefania Berton and Ondrej Hotarek were third with 59.79.
Skate Canada International is the second stop on the ISU Grand Prix circuit that culminates in the Grand Prix Final, Dec, 6-9 in Sochi, Russia.