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 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 (UKR) with the winning lead and elevated Sheppard to fourth.
The Kiwi flew down the technical descent to pip Neethling and claim third place.
Sheppard now has a break for a month until her next race, with her performances over the past 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 suffered two punctures, one on the first lap and another with the finish almost in sight, but did well to fight his way 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 six riders.
