Wendl and Arlt looked to be well on their way to a sixth straight World Cup win from the six rounds so far this season and first career European title on home ice after posting the quickest time of round one on home ice.
They even set a start record on run two in Oberhof however they lost speed thereafter in comparison to Eggert and Benecken, who after three second places and a third this season, finally claimed a victory.
With the Oberhof World Cup also doubling up as the European Championships, Eggert and Benecken claimed their maiden continental title as well while Wendl and Arlt were left with silver for the third time running.
Eggert and Benecken, third at the Europeans last year, clocked an overall winning time of 1:23.240minutes for first place with Wendl and Arlt, who set a start record of 6.520seconds on run two, just 0.022 behind in the runners-up spot.
Peter Penz and Georg Fischler, the defending European champions, did enough to claim third 0.224 behind Eggert and Benecken but 0.126 ahead of Italian's Christian Oberstolz and Patrick Gruber in fourth.
However the result sees the Austrian duo fall from second in the overall rankings to third being overtaken by Eggert and Benecken who decrease Wendl and Arlt's lead from 130 points to 118.