Four straight wins and a second has put Frenzel into contention for the overall World Cup title and, despite not competing in Kazakhstan, Kircheisen ensured the German success kept coming.
Kircheisen made up nearly a minute deficit after ranking ninth in the ski jump to beat Akito Watabe by just over five seconds for his first victory of the season and 16th individual one of his career.
The 29-year-old produced the quickest cross country time for an overall winning effort of 25:09.6minutes with Watabe second and Austria's Christoph Bieler third.
Mario Seidl led after the ski jumping after recording 125.2 points with Watabe's Japanese teammate Taihei Kato second with 122.0 and then Bieler in third with 121.3.
Kircheisen was down in ninth with 110.7 giving him a 58-second deficit to make up on Seidl, something he managed to do as the Austrian fell to fifth overall.
The German clocked 24:11.6 for his cross country ski with Watabe clocking the fifth quickest time to move into second while Bieler held onto third despite being the 12th fastest.
Despite none of the top five in the overall World Cup standings competing in Almaty there is no change to the overall order with Frenzel still leading ahead of Lamy Chappuis.
A second event follows in Kazakhstan before a break for the Nordic Ski World Championships and then the final three rounds in Scandinavia in March.