The 27-year-old Norwegian timed his move to the finish to perfection in the final with less than half a second separating the six-strong field for much of the race.
Northug's winning margin may have only been 0.7 seconds ahead of compatriot Eirik Brandsdal but it was a comfortable victory in the first of four events at the World Cup Final.
Russian Olympic and world sprint champion Nikita Kriukov was a further 0.4 seconds adrift in third with Northug knocking his team-mate Alexander Legkov off top spot overall with the win.
Legkov took the lead after his victory in the 50km freestyle mass start on Saturday but he didn't make it out of the quarter-finals as he picked up just four points.
Northug meanwhile took 50 and 60 bonus seconds heading into the second event of the four-stage finale the individual prologue, which takes place in Falun.
He leads Legkov by 34 points with defending champion Dario Cologna nine behind in third and admitted to being satisfied with his day's work in Stockholm.
"I started a little bit slower in every heat. I was trying to find the right position and it was not as windy behind at the back," said Northug.
"The goal in every heat was to have a good position before the last climb up to the finish and that I managed."
Meanwhile Justyna Kowalczyk, who already has the overall women's World Cup title wrapped up, won the last sprint of the season amid freezing conditions in Stockholm.
Kowalczyk took the lead just over a third of the way into the ladies' sprint and was aided by Mona-Lisa Malvalehto's fall which disrupted those chasing behind her.
Everyone apart from Kowalczyk was caught up in the field with Marit Bjoergen, who was at the back at the time, having to muscle her way past before moving up to second.
She battled valiantly to overhaul Kowalczyk but the World Cup champion was just too far ahead clocking a winning time of 2:45.8 in Stockholm.
Bjoergen finished 2.2 seconds behind in second with Kerttu Niskanen the best of three Finnish skiers involved in the final placing third another 0.9 further adrift.
And Kowalczyk said: "It was not so hard. I skied really good and this was my day. I like the cold conditions, they are good for me, and it was perfect."