The tournament, seen as a key step on the road to the Pyeongchang Winter Olympics in two months, lacked the presence of two-time world champion and fellow Russian Evgenia Medvedeva, widely seen as a favourite for Olympic gold, after she qualified but then withdrew with a fractured bone in her foot.
The 15-year-old Zagitova, who last year won the Junior Grand Prix Final, overcame several wobbles on landings to win with a jump-laden routine to "Don Quixote."
Snapping off a clean triple lutz-triple loop combination, as well as a sharp triple Salchow and triple flip in the second half of her routine, Zagitova hit a season's best with a total of 223.30.
"There were a number of small mistakes but they weren't that big a deal. I'm very happy to have won at the Grand Prix," she said just after winning her title.
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Asked how she managed to keep her stamina up for the unusually jump-heavy second half of her free programme, Zagitova told a news conference that it had taken time to adjust.
"For this programme I wasn't so confident I could skate to the end because in the middle, in the (step) sequence, I'd get tired," she said.
"But my coaches believed in me and said 'you can do it,' and that gave me confidence, and I was finally able to skate to the end."
Fellow Russian Maria Sotskova came second with 216.28 while Canadian Kaetlyn Osmond came third.
In ice dancing, the French team edged ahead of Virtue and Moir with an elegant, passionate routine to "Moonlight Sonata," winning with 202.16 to 199.86 for the Canadians.
"We're relieved that it's done," Cizeron told a news conference. "We had a good skate."
Later, referring to the looks he gave Papadakis during the routine, he told a small group of reporters: "We have to skate with someone as if we were one person, and we have to be really, really connected."
Two-time Olympians Virtue and Moir, who topped the podium in Vancouver in 2010, had racked up win after win since their return to competition with Skate Canada 2016. At Skate Canada this year they set a new record score.
"We're not going to hang our heads, we're going to go home and work," Moir told a news conference.
Germany's Aljona Savchenko and Bruno Massot took gold for pairs with an ambitious, elegiac free skate to "La Terre Vue du Ciel" by Armand Amar, snagging a season's best 236.68 overall. China's Wenjing Sui and Cong Han won silver with 230.89 after a wobble on a triple Salchow, while Meagan Duhamel and Eric Radford of Canada came third with 210.83.
(Reporting by Elaine Lies; editing by Clelia Oziel)
