Bjoergen, winner of the opening Royal Palace Sprint in central Stockholm two days ago, climbed the infamous "Mordarbacken" (Murder Hill) to finish in 6 minutes and 54.4 seconds.
Sweden's Charlotte Kalla was second, 6.2 seconds behind. Norwegian Marthe Kristoffersen was third, 11.4 behind Bjoergen.
With the win Bjoergen leads the four-stage event by 21.5 seconds from Kalla in second place. The Norwegian also extended her overall World Cup lead to 170 points over Poland's Justyna Kowalczyk, the only other skier still in contention for the title.
Kowalczyk, overall winner the last three seasons, is fourth in the event, 46.5 seconds behind Bjoergen.
"I had a very good feeling from the start," said Bjoergen. "I went fast up Mordarbacken and then I knew I could take some seconds also in the downhill section.
"After two stages I am where I wanted to be. I have many seconds on Justyna Kowalczyk, it can be that Charlotte (Kalla) and I will be competing for the World Cup Final victory. But it's classic tomorrow and it will be important to have good skis."