Maltais, from Petite-Riviere-St-François, Que., overtook and held off Lindsey Jacobellis to edge out the American and win the women's final under sunny skies in the Pyrenees mountains. Raffaella Brutto of Italy finished third after Yuka Fujimori of Japan crashed.
Maltais, who won the silver medal at the Sochi Olympics, finished the season with 5,400 points. Jacobellis was next with 3,760, followed by Alexandra Jekova of Bulgaria with 2,850.
"I knew that the crystal globe was waiting for me already," Maltais said. "But I love what I do, so I really wanted to end the season on a good way. I'm very happy about my career's fifth title."
Maltais called it a "great race on a great course."
"It was tight racing from quarter-finals through finals," she said. "I pushed myself a lot because I wanted to finish the season with a big win."
Paul Berg of Germany earned his first career individual win.
Berg rode flawlessly to finish ahead of Olympic silver medallist Nikolay Olyunin, with Spaniard Regino Hernandez coming third after he and Calgary's Christopher Robanske slowed each other down early in the descent.
On Friday, Omar Visintin of Italy claimed the men's season title when Australian Jarryd Hughes, the only rider with a chance to overtake Visintin in the standings, failed to qualify.
Visintin didn't advance beyond Saturday's quarter-finals. Olympic champion Pierre Vaultier of France fell early in the round of 16.
Berg and Robanske both moved ahead of Hughes in the standings. Berg's win lifted him into second place to end the season with 2,150 points, behind Visintin's 3,076. Robanske ended the campaign in third with 2,120.
"I'm speechless," Berg said. "Yesterday, I was happy about my good result in the qualifications. Today, I just wanted to go for it and challenge the big names. I never thought about winning a World Cup this season. It's still such a surprise."