Sheppard said she wanted to stamp her dominance on the race.
"The rain came through just before we started which made the course super slippery. I tried to find a rhythm and ride smart or when it wasn't possible to ride, get off and run. I got out in front and rode my own race."
She beat a talented field including world cup leader Yana Belomoyna (UKR), a two-time winner this year.
"Definitely it was a tough field as all the world cup races are. But I always love coming here. It is a really tough track and I think everyone loves it to be honest. It's got everything. It is so physical. You can't let up or you will crash."
Sheppard believes the win will prove a turning point for her.
"To come here to do it on my favourite track is great. It shows I've been training really well. We've got a good programme going into the worlds and everything is coming together nicely. Basing myself in Europe and with the Wheeler ISC team support, I am really happy with how things are going.
"Once I got on the podium at the last round then I started to believe in myself more, and now I know I can go out there and win. It definitely gives me a lot more confidence for the rest of the season leading into (the world championships in September)."
The victory moves Sheppard to third overall on the world cup standings with two rounds remaining.
Johnston, the Oceania under-19 champion, grabbed third place in the junior women's race after holding off Canada's Rachel Pageau in a sprint finish for third place. She finished only 2:39 from winner Frederique Tredel (CAN) in her first world cup start.
Teammate Samantha Hope (Dunedin) finished eighth.
Earlier, Brad Hudson (Christchurch) and Tom Bradshaw (Palmerston North) finished mid-pack in the men's under-23 race.
Manawatu's Mathew Waghorn made a strong start and by lap three had forced his way through the pack. But he crashed on one of the slippery descents and was also forced to make a tyre change, before his replacement tyre got slashed on a sharp rock on the following lap to end his chances.
Hudson was caught in a bunch start but slowly worked his way through the field to be leading kiwi in 34th while Bradshaw made a fast start before fading on the tough climbs to finish 37th.
"It is definitely good to have a World Cup start under my belt, I will be doing things a little differently next weekend," Hudson said. "The experience is invaluable no matter what happens, but I am really looking forward to a better result next weekend."
Bradshaw's introduction to world cup racing proved an invaluable experience.
"It was a good eye-opener for me about where my riding is at. I knew it would be hard coming over from the New Zealand winter and racing all the Europeans, but that is why we are here, because it is hard."
Results:
Under-23 women: Samara Sheppard (NZL, Wheeler IXS) 1:22.18, 1; Yana Belomoyna (UKR) 1:34.29, 2; Rebecca Henderson (AUS) 1:35.48, 3.
Under-23 men: Michiel Van der Heijden (NED) 1:26.57, 1; Gerhard Kerschbaumer (ITA) 1:27.31, 2; Markus Schulte-Leunzum (GER) 1:28.46, 3. Also New Zealanders: Brad Hudson (Christchurch) 1:39.19, 34; Tom Bradshaw 1:42.47, 37; Mathew Waghorn dnf.
Junior women: Frederique Trudel (CAN) 1:18.30, 1; Dina Hordiyuk (UKR) 1:19.32, 2; Amber Johnston (NZL) 1:21.09, 3. Also: Samantha Hope (NZL) 1:26.46, 8.
Elite women: Catharine Pendrel (CAN) 1:41.40, 1; Georgia Gould (USA) 1:42.03, 2; Marie-Helene Premont (CAN) 1:43.31, 3.
Elite men: Nino Schurter (SUI) 1:41.24, 1; Jose Hermida Ramos (ESP) 1:41.24, 2; Jaroslav Kulhavy (CZE) 1:43.13, 3.
