Northug cruised to victory in the sprint in Stockholm on Wednesday to leapfrog Alexander Legkov in the race for the overall Crystal Globe and then built on it in the prologue in Falun.
The 27-year-old led home a Norwegian one-two-three, clocking a winning time of 5:20.7 minutes with Paal Golberg second, 2.1 seconds adrift, and Anders Gloeersen third another 0.8 behind.
Legkov ranked ninth with Sweden's Calle Halfvarsson fourth and then Martin Johnsrud Sundby, Finn Haagen Krogh and Eirik Brandsdal.
Marcus Hellner was then eighth before Legkov, who drops to 22nd in the mini tour standings, while Northug leads Brandsdal by 27.3 seconds with the 15km classic mass start next up on Saturday.
Northug now has 1321 points with his lead over Legkov growing from 34 to 56 with defending champion Dario Cologna, who was 11th in the prologue, third with 1252.