Marquis, from Quebec City, finished ahead of Sho Endo of Japan for his first World Cup title in two years.
"There were several tough duals today," said Marquis. "Everyone was skiing pretty well. Skiing smart was the key to my success and to make it possible for me to win gold. It's really great to start the year on this note."
Anthony Benna of France won the bronze.
Yulia Galysheva of Kazakhstan won the women's competition. Dufour-Lapointe, from Montreal, finished second and American Hannah Kearney took the bronze.
Originally scheduled as a moguls competition, the event was change to duals just two weeks ago.
"We started off with a duals competition (this year) so it was a little bit scary," said Dufour-Lapointe. "But I ended up having so much fun on this course and finishing second.
"I'm really happy to start my season this way."
Audrey Robichaud of Quebec City was fourth, Justine Dufour-Lapointe of Montreal was fifth and Regina native Andi Naude was sixth.
Reigning Crystal Globe champion Mikael Kingsbury of Deux-Montagnes, Que., was well back in ninth.
"It's just the beginning," said Kingsbury. "I lost my dual due to a mistake. It happens to the best athletes in the world. I don't want to change anything, I just want to come back strong.
"Phil was killing it today though. I'm very happy for my friend. We trained all summer together."Suggest a correction