The 19-year-old was on form from the off on Blue Mountain, winning her quarter-final and semi-final before repeating the trick to deny a home win in the big final.
Samkova beat Maltais, who was victorious in Montafon and Telluride, for her first defeat this season while Nelly Moenne Loccoz took third ahead of another Canadian Maelle Ricker.
And, while she was defeated, Maltais did extend her lead in the overall snowboard cross World Cup standings to 1300 points ahead of Olympic champion Ricker with Samkova now third.
Britain's Zoe Gillings didn't make it out of the quarter-finals on Blue Mountain, placing 15th overall, while Chris Robanske also took his first win of the season in the men's event.
Much like in the women's event, Robanske ensured the World Cup leader, this time Australian Alex Pullin, had to make do with second place, while Nick Baumgartner was third.
Markus Schairer finished fourth in the men's big final with Pullin's overall lead cut to 320 points by Robanske, who now sits in second place with a total of 1780.