The British rider, 29, dislocated her shoulder in a crash during a practice run on the morning of the race.
Atherton, who had won 14 races in a row since 2015, said on Instagram she was "absolutely devastated".
Australia's Tracey Hannah won the race, with Britain's Manon Carpenter fourth.
The next round in the UCI downhill World Cup takes place in Leogang, Austria on 10-11 June.
World champion Rachel Atherton's two-year UCI downhill Mountain Bike World Cup winning run came to an end on Sunday when she missed the race at Fort William, Scotland through injury.