Swiss star Schurter came into the most gruelling race of the 2018 calendar looking to seal a sixth XCO crown, however, he was under pressure from the start.
He battled back to look comfortable, but a broken chain and then a rear flat tyre meant he could only finish seventh which was still enough for a sixth title.
Schurter, 32, revealed: "Super stressful from the beginning. I broke my chain and I am still happy with my performance. Big challenge now with young, new riders pushing hard."
Up front, his compatriot Mathias Flueckiger captured his maiden victory after Kiwi Anton Cooper crashed on the last lap with Italian Gerhard Kerschbaumer and France's Titouan Carod rounding out the top three.
Flueckiger, 29, said: "I am so happy. So much bad luck before. It is something special as I won the U23 world title here in 2010. I hope Anton is OK."
World champion Neff rode superbly in the heat to record her third Mont-Sainte-Anne win, just days after European Championship XCO gold in Scotland.
Denmark's Annika Langvad held off home hero Emily Batty for second with the title going down to the final La Bresse race as Neff holds a 142-point lead seeking her third overall crown after 2014 and 2015 wins.
Neff, 25, said: "It still feels like a dream this week. In the third lap, I was done. I had to tell myself to slow down as the heat was so extreme. The last two times I won here, I won overall too."
Langvad, 34, added: "I struggled so badly on the climbs. It doesn't change much for La Bresse. Race for the victory. Go into it with a clear mind and do my best."
1. Jolanda Neff SUI 1:29:27
2. Annika Langvad DEN +1.52
3. Emily Batty CAN +2.06
Women's overall cross-country standings:
1. Jolanda Neff SUI 1600 points
2. Annika Langvad DEN 1458
3. Maja Wloszczowska POL 1077
Men's cross-country result:
1. Mathias Flueckiger SUI 1:27:26
2. Gerhard Kerschbaumer ITA +0.15
3. Titouan Carod FRA +0.23
Men's overall cross-country standings:
1. Nino Schurter SUI 1546 points
2. Mathieu van der Poel NED 1080
3. Henrique Avancini BRA 1061