The Austrian led after the first round of action with a blistering run of 50.084seconds and as the snow fell heavily, the second run was subsequently cancelled due to poor visibility.
That left Egger as the winner, his first victory at World Cup level after two podiums already this season – in Whistler and Lake Placid.
Germany hold off Austria to claim World Cup relay event in Konigssee
Second on the day was Italy's Dominik Fischnaller while Germany's Sebastian Bley took third.
Egger climbs to fifth in the overall standings with the victory while Johannes Ludwig remains on top.
Roman Repilov – winner of the last two events in Lake Placid – was fifth in Konigssee and stays second overall, defending World Cup champion Felix Loch is fourth.
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