Kim won the last mass start event in Kolomna to pull within ten points of World Cup leader Mariska Huisman with another victory in Germany putting her top.
The 20-year-old was the first to cross the finish line in 8:13.80minutes, 0.30seconds ahead of Francesca Lollobrigida with Huisman third another 0.01 adrift.
Kim goes from trailing by ten points to leading by 20 over Huisman with a total of 260 while Canada's Ivanie Blondin, who was fifth in Inzell, is third with 180.
Meanwhile Marrit Leenstra also moved from second overall to first in Germany, this time in the ladies' 1500m despite finishing down in sixth.
European all-round champion Ireen Wust clocked 1:55.95 for victory, 0.47 ahead of Dutch teammate Diane Valkenburg while Russia's Yekaterina Shikhova was third.
However with previous leader and Olympic 1000m champion Christine Nesbitt not in Inzell, Leenstra's sixth-place finish, 1.78 behind Wust, gives her a 35-point lead at the top of the rankings.
And Sven Kramer, who like Wust won the European all-around title earlier this year, took the win in the men's 5000m and his third from four events this season.
Kramer was the clear victor of a Dutch one-two-three as he clocked 6:11.76 for a winning margin of 2.32 over Bob de Jong with Jorrit Bergsma behind both in third.
Third was enough for Bergsma to maintain the overall World Cup lead in the 5000m with Kramer, who as absent from the third race in Astana, 20 points behind him in second.