She slipped back to fourth on lap one and by lap two was fifth, nearly five minutes behind the leader, Swiss teammate Jolanda Neff who won the last round.
The New Zealander was still in fifth at the start of the final lap and 44 seconds behind South Africa's Candice Neethling but she had reduced the gap to 18 seconds by the halfway point.
Neff crashed out of the race after falling heavily on the descent on the final lap which presented the world cup leader Yana Belomoyna (Ukraine) with the winning lead and elevated Sheppard up to fourth.
The kiwi flew down the technical descent to pip Neethling in the sprint to claim third place.
Sheppard now has a break for a month until her next race, with her performances over the last two weeks cementing her qualification for September's world championships.
Meanwhile, the Rotorua pair of Dirk Peters and Sam Shaw finished 38th and 48th respectively from 91 starters in the men's under-23 race.
Peters, like last week in the Czech Republic World Cup, started conservatively to be near the nail of the field after the start loop.
He had to force his way through the field on a compact course, moving up to 63rd on lap one, 48th on lap two and ultimately up to 38th.
Shaw had a solid start to be 54th on the opening lap, a position he held until a flying final lap where he passed seven riders.
More than 20,000 fans have thronged to the venue in readiness for tomorrow's (mon) elite races with Whakatane's Karen Hanlen is the only kiwi racing in the elite women's race after Olympic rival Rosara Joseph broke her wrist after crashing in practice.
Results, UCI Mountain Bike World Cup, La Bresse, France:
Under-23 women: Yana Belomayna (UKR) 1:23.33, 1; Rebecca Henderson (AUS) at 1:37, 2; Samara Sheppard (NZL) at 2:21, 3; Candice Neethling (ZAF) at 2:22, 4.
Under-23 Men: Alexander Gehbauer (AUT) 1:22.24, 1; Markus Schulte-Luenzum (GER) at 1:22, 2; Mattias Stirnemann (SUI) at 2:01, 3. Also New Zealanders: Dirk Peters at 8:40, 38; San Shaw at 11:22, 48.
APNZ dr
