German Thees has been the most consistent slider during a wide open World Cup season so far and took to the Altenberg track leading by just 14 points ahead of Canadian Sarah Reid.
However she ensured the gap between her and the rest of the field grew wider as she staged a fine comeback to claim her fourth top-three finish of the season on home ice and second win.
Thees was trailing both teammate Anja Huber and defending world champion Katie Uhlaender in second and first respectively after posting a time of 1:00.35minutes during her first run.
Uhlaender led by 0.17seconds ahead of Huber with Thees a further 0.06 adrift although the tide was to be turned after the second run with the American missing out by the narrowest of margins.
With times significantly slower, Thees clocked the best, 1:02.24, to jump from third to first with Uhlaender going 0.24 slower than the German to miss out on her third victory of the season by 0.01.
Huber fell to fifth after a poor second outing to allow Uhlaender's American teammate Noelle Pikus-Pace to move up a place to third and world bronze medallist Yarnold follow suit to fourth.
Pikus-Pace clocked 2:02.87 overall to finish third, 0.27 behind Uhlaender, with Yarnold just 0.06 behind in fourth for a third consecutive race without finishing in the top three.
She was again clear the best Brit though with reigning World Cup champion Shelley Rudman and Donna Creighton going in opposite directions in Altenberg.
Rudman was ninth after the first run but dropped to 16th, by far her worst finish of the season so far, while Creighton impressed in going from 15th to seventh.
Creighton has struggled for form after finishing fourth at the World Cup opener in Lake Placid but seventh is a vast improvement and marks her second-best finish of the season.