Jacob, who turned 20 in August and was making his tenth World Cup start, won a six-strong big final in Andorra with Norway's Stian Sivertzen second and Italian Omar Visintin third.
American duo Nate Holland and Nick Baumgartner were pushed off the podium with another Italian in Emanuel Perathoner separating the two as he finished in fifth place.
Australian Jarryd Hughes, victorious last time out in Lake Louise, was fifth in the small final for 11th but leads the overall snowboardcross World Cup standings ahead of Visintin and Sivertzen.
Meanwhile, in contrast to Jacob, Maltais claimed the 12th World Cup victory of her career and first of the season having been runner-up in Montafon and Lake Louise in December.
Alexandra Jekova placed second in the big final and Lindsey Jacobellis third with Maltais leading the snowboardcross World Cup standings by 640 points ahead of the latter.
Great Britain's Zoe Gillings recorded her lowest finish of the season as she placed 17th overall, she is tenth in the overall standings with 790 points.