The Briton, who rides on the road for INEOS Grenadiers, finished fourth in the cross-country race after tangling with a tree and needing a wheel change on the penultimate lap.
Pidcock had moved through the field to lead on lap three.
The multi-disciplined rider from Leeds produced a masterclass to win gold in Tokyo last year and last week became the first Briton to win the European title in the event.
Swiss veteran Nino Schurter (36) won the title for a 10th time with Spain's David Valero Serrano second.
Pauline Ferrand Prevot delighted the home crowd by winning the women's title, her second title in 48 hours after winning the short track championships and her fourth overall.
Pidcock won a stage of the Tour de France in July, climbing the mythical Alpe D'Huez first - finishing in Paris 17th overall. In January, he won the world cyclo-cross world championships in Fayetteville, USA in what has been a remarkable year for him.