Moller has been part of a German dominance this season, heading to the seventh round and fifth and final one on home soil third in the overall standings behind Loch and Andi Langenhan.
And the 31-year-old, who won Olympic silver at Vancouver 2010, ensured it was his turn to taste victory again in Winterberg, his second from the last three rounds.
He went from third after run one to first after run two with a track record of 52.047seconds with Loch second and ten-time overall World Cup winner Armin Zoeggeler third.
The result actually benefits Loch's cause at the top of the standings though with his lead extending from 80 points to 102 with Langenhan finishing down in sixth in Winterberg.
Moller occupies second place with Langenhan third, 13 points behind, with the final two rounds in Lake Placid and Sochi at the start and end of February respectively.
It was Italian Zoeggeler who led following the first runs after clocking 52.061 with Loch second with an effort of 52.146 and Moller third just 0.014 behind his German teammate.
However Zoeggeler was to swap positions with Moller following the second runs as the German set a track record of 52.047 for an overall winning time of 1:44.207minutes.
Loch clocked 52.070 to finish just 0.009 behind in second with Zoeggeler not too far off himself, 0.053 shy, before three more Germans, Julian von Schleinitz, Johannes Ludwig and Langenhan in fourth, fifth and sixth respectively.