The two-time Olympic champion – thanks to an untimely tumble – ended the sprint final in last place but with previous leader Axel Teichmann unable to make the final the overall lead belonged to the Norwegian.
Dario Cologna was fifth in the final and sits second in the standings behind Northug while Japarov’s fourth-place finish was enough to lift him to third overall.
In the women’s 1.2 km sprint Justyna Kowalczyk continued her unstoppable start to Tour de Ski by claiming her third victory in as many days to top the standings.
Norwegian cross-country darling Marit Bjoergen’s was unable to live with her Polish rival in the last ascent and was forced to settle for second, just over three seconds back.
Bjoergen’s compatriot Astrid Jacobsen was third but there was the field just couldn’t live with the in-form Kowalczyk as she took her ninth overall Tour de Ski stage victory in Oberstdorf.
Her third win on the bounce predictably leaves Kowalczyk at the head of the overall Tour de Ski standings with Bjoergen in second and Therese Johaug third.