Chartrand was in first place after the short program but fell two positions with a free skate where several jumps were underrotated.
"I felt really uptight and the skating wasn't as good as I wanted it to be," she said. "Mostly the biggest errors were the landings on the jumps."
The 18-year-old was still pleased with her personal-best score of 172.00.
''Definitely I reached a new level today to win a medal in my first season on the senior Grand Prix,'' Chartrand said. ''I didn't feel any extra pressure today because I had won the short program. I'm always nervous anyway.''
Chartrand, from Prescott, Ont., was seventh at Skate Canada two weeks ago.
Hongo's free skate to music from the opera Carmen featured seven triples including an opening flip-toe loop combination. The 18-year-old is also in her first year of seniors competition.
Anna Pogorilaya of Russia, who won at Skate Canada two weeks ago, took silver despite a troubled program in which her hand went to the ice on three jumps.
The gold was Hongo's first medal in the Grand Prix series. Her accomplished performance could raise the temptation to fancy being the next big thing in Japan's long line of standout skaters, but Hongo said she isn't ready to think that way.
"I really haven't thought about that," she said. "I am trying hard to get closer to skaters like Mao Asada."
Hongo had 178.00 points and Pogorilaya had 173.43 points.
Pogorilaya suggested she may be experiencing the opposite of a home advantage, noting that she generally performs better abroad.
"I felt some kind of pressure ... I can't really fathom it," she said.
In the men's competition, the wait was a little hard for Javier Fernandez as the last skater to get on the ice, but he overcame it to win his second Grand Prix gold medal.
As the leader after the short program, the Spaniard had to worry about seeing strong free skate performances from Sergei Voronov and Michal Brezina and about losing the sharpness from his warmup.
"When I got onto the ice, (my) legs were not the same after waiting for a long time," he said.
His confident opening quad toe loop gave no hint of concerns, though he stepped out of his following quad salchow and put his hand to the ice on a third quad attempt. But his exuberant skating to strains of The Barber of Seville ended with him 13 points ahead of Voronov.
Brezina nailed a quad-double combination early on that helped power the Czech skater to bronze, aided by the falls and popped jumps that dropped Japan's Takahiko Kozuka from third place to sixth.
Jeremy Ten of Vancouver was 10th.
''I came here to introduce my quad jump into the program and for me that was a success,'' said Ten. ''I gained confidence that it's a jump that I have the ability to land, hopefully at my next competition. I was also pleased with how I came back with a strong triple Axel today as well.''
In pairs, Russians swept the podium. Ksenia Stolbova and Fedor Klimov won with a dramatic and taxing free skate to Notre Dame de Paris music, followed by Evgenia Tarasova and Vladimir Morozov and the duo of Kristina Astakhova and Alexei Rogonov.
Americans Haven Denney and Brandon Frazier earned the second-highest free program marks, but ended just 0.01 points short of a medal.
Megan Chock and Evan Bates of the United States took gold in ice dance, followed by Elena Ilinykh and Ruslan Zhinganshin of Russia and Britain's Penny Coomes and Nicholas Buckland.
It was the Americans' second Grand Prix gold of the season and "looking back on Skate America, this was a step forward," Bates said of their free dance to An American in Paris. "Emotionally it felt better."
With files from The Canadian Press.