The 30-year-old, who hails from just 50km away in Bavaria, is a four-time Olympic champion and boasts the most World Cup stage victories of all time with 47.
But constant, thick snow made conditions nigh-on impossible for the German whose equipment set-up appeared wrong in a first run that left her 15th.
Geisenberger recovered somewhat with 53.085s at the second time of asking, but was undermined by the track not being cleared of snow for over five minutes before her run.
Geisenberger crowned champion in dramatic World Cup finale
She left the leader's box at the earliest stage ever in a World Cup race when Latvia's Eliza Cauce surged ahead.
For the first time in 2018-19 there was only one German on the podium, Julia Taubitz winning her second World Cup stage of the season with 1:44.971s overall.
USA's Summer Britcher finished second in the snow, while Austria's Hannah Prock claimed a first World Cup podium of her career with bronze.
Geisenberger maintained her overall World Cup lead with 612 points with compatriot Taubitz second on 595.
Sigulda, Latvia provides the sixth stage of World Cup action next weekend.
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