The American, who secured a spot at Sochi next month with his second-place finish, bettered Bilodeau in both time and turning scores.
But the Canadian's jump combination of a back double full off the top and an off-axis 1080 on the bottom jump were enough for him to take the win by three tenths of a point with a score of 25.72.
Bronze went to USA's Bradley Wilson, who bettered his brother Bryon by 0.2 of a point to record his first podium of the season.
While Bilodeau's team-mate Mikael Kingsbury, winner of the first three World Cups, was sixth, leaving Bilodeau to leapfrog him into top spot in the overall standings by 20 points.
Bilodeau said: "It's nice to have the yellow bib back, but my party is the Olympics. I did a couple mistakes today. I'm feeling good on my skis but there's still a place for improvement and I'll build up on that.
"I know my colleague Mikael (Kingsbury) won't do those mistakes much with the Olympics coming up, so I need to step it up again."
It was also a Canadian victory in the women's event as Justine Dufour-Lapointe recovered from a poor qualification score to lay down strong runs in the finals and superfinals for her second victory of the season.
Her score of 23.90 saw her take gold, ahead of USA's Heidi Kloser who took a career best result in second, while Hannah Kearney was third.
The latter retains the overall standings lead with an 84 point lead over Dufour-Lapointe on 356 points.