Courtney won the 2019 season opener in Albstadt last week to become the first American woman to win an XCO race in 20 years and she started brightly again.
Dutch rider Anne Tauber looked in control towards the finish, however suffered a bent rear derailleur on the final lap to let Courtney in for back-to-back wins.
Australian Rebecca Ellen McConnell and Canada's Haley Smith both had career best finishes in second and third with Tauber 10th and Sweden's Jenny Rissveds 30th on her emotional UCI MTB World Cup return from depression at the scene of her 2016 World U23 triumph.
Courtney, 23, said: "I am so gutted to see her (Anne) have an incident in the last lap. I was just trying to stay focused on riding clean lines. When I had my flat it was a little bit of a tough mental day, but I was able to reset and focus on my own pace."
Tauber added: "I am not really sad, but really angry at myself because I am in good shape. I have improved a lot technically, but I don't know how to win yet."
In the men's race, Van der Poel produced a brilliant surge to finally get the better of rival Schurter and record his first UCI World Cup win on a mountain bike.
The Dutchman tracked the six-time World Cup champion for the first half, then used an uphill surge on the last lap to create a winning gap.
Van der Poel, 24, revealed: "It is extra sweet against one of the greatest mountain bikers. I went all in and I am really happy to finally take that World Cup win."
World champion Schurter, 33, added: "I tried to break him over the last three laps, but he was just too strong today. It was the best possible result for me."
1. Kate Courtney USA 1hr27m31s
2. Rebecca Ellen McConnell AUS +0.36
3. Haley Smith CAN +0.42
4. Sina Frei SUI +0.45
5. Malene Degn DEN +1.33
10. Anne Tauber NED +2.38
30. Jenny Rissveds SWE +1 lap
UCI MTB World Cup women's XCO overall standings:
1. Kate Courtney USA 700pts
2. Jolanda Neff SUI 490
3. Chloe Woodruff USA 385
4. Rebecca Ellen McConnell AUS 378
5. Anne Tauber NED 350
Men's XCO Nové Mesto top-five results:
1. Mathieu van der Poel NED 1hr21m54s
2. Nino Schurter SUI +0.19
3. Mathias Flueckiger SUI +1.53
4. Henrique Avancini BRA +2.01
5. Ondrej Cink CZE +2.12
UCI MTB World Cup men's XCO overall standings:
1. Mathieu van der Poel NED 700pts
2. Mathias Flueckiger SUI 500
3. Nino Schurter SUI 485
4. Maxime Marotte FRA 425
5. Henrique Avancini BRA 370