The 16-year-old from Estonia claimed her first ISU international title ahead of Alexia Paganini and Jenni Saarinen.
Estonia's Eva-Lotta Kiibus took victory at the Nebelhorn Trophy on Saturday (26 September).
Lying third after the short program, the 16-year-old made fewer mistakes than her rivals to move up to top spot and claim her first Challenger Series title.
Switzerland's Alexia Paganini - the short program leader and pre-event favourite - had a number of jumping errors and slipped to second place.
Jenni Saarinen of Finland filled the last place on the podium.
For Kiibus, who was denied an appearance at her first World Championships due to the coronavirus pandemic, it was her maiden triumph outside of her homeland.
In this first international event of the delayed 2020/21 figure skating season, the skaters could be forgiven for showing signs of rustiness particularly in the jumping department.
And with no crowd due to Covid-19 restrictions, there was a distinct lack of atmosphere for the women.
Jenni Saarinen was fourth after the short program and set the target for those to come.
Despite falling on her opening triple Lutz, the Finn was able to put together a decent routine although her free skate score of 106.62 was some way short of her best as she posted a total of 163.87.
Next up was Kiibus who, while far from foot-perfect, took the lead thanks to her performance to Rachmaninov's Piano Concerto No.2 in C minor.
The Estonian - seventh at January's European Championships - was rewarded for some strong elements in the second half of her routine including a triple Lutz-double toe loop combination.
She scored 113.04 to go into the lead overall on 173.53.
Nicole Schott, who lay second after a personal best in the short program, was unable to keep that form going in the free skate.
The German skater, based in Oberstdorf, really would have benefited from a local crowd to encourage her as her confidence in her jumping visibly ebbed away.
She moved into third place with just one skater to come.
After her fourth place at the European Championships - with only Russian trio Alena Kostornaia, Anna Shcherbakova and Alexandra Trusova in front of her - Alexia Paganini was widely expected to win this event.
But the PyeongChang 2018 Olympian, coached by Stephane Lambiel who enjoyed success with Deniss Vasiljevs in the men's singles on Friday, made a poor start to her free skate with falls on her opening two jumps.
The 18-year-old managed to get back on track and impressed with her artistic interpretation of music from the soundtrack to Pedro Almodovar's Hable con Ella (Talk To Her).
However, jumping issues continued to dog her with a triple loop-double toe loop-double loop combination not receiving anything like the score she would have wanted.
At the end of the routine, blood was visible on her right hand at the end after contact with a skate blade.
Paganini's score of 105.25 was third in the free skate, enough for second overall on 168.85, as Kiibus claimed the biggest win of her young career.
PyeongChang 2018 pairs gold medallist Aljona Savchenko was on coaching duty in Oberstdorf, guiding German youngster Aya Hatakawa.
The Dusseldorf-born 16-year-old was 12th in the free skate to take 16th overall.