Running in reverse order, it came down to the wire. Fitzsimon had to go double clear and faster than Scott's 58.34-second effort to win the final.
Fitzsimon came out firing, and they crossed the flags in 57.46 seconds.
The win gave Fitzsimon, 31, a perfect score in the series, which counts a combination's best four finishes, with four victories from five starts.
Windermere Cappuccino was out with injury for last season's final, making this year's win all the more special, Fitzsimon said.
“I am so thankful to have the ride on him and share joint ownership with the Parkes family.”
The winning combination of the series has the opportunity to represent New Zealand at the final in Leipzig, Germany, in April — should it go ahead.
The World Cup series is the highest-ranked international competition in New Zealand.
POLi Payments FEI World Cup (NZ League) Final: Tegan Fitzsimon (West Melton) Windermere Cappuccino 1, Sophie Scott (Palmerston North) Waitangi Skynet 2, Sophie Scott (Palmerston North)Glenbrooke Rich as Roses 3, Vicki Prendergast (Matamata) Selena C 4, Maurice Beatson (Dannevirke) Central Park 5, Melody Matheson (Havelock North) Cortaflex Enya MH 6.
POLi Payments FEI World Cup (NZ League) Series (best four to count): Tegan Fitzsimon (West Melton) 90 points 1, Maurice Beatson (Dannevirke) 68pts 2, Sophie Scott (Palmerston North) 64pts 3.