Roenning got the better of Russian Maxim Vylegzhanin and Norwegian team-mate Martin Johnsrud Sundby on the home straight of the 15km classic mass start in Sweden.
All three broke off from a leading pack of five over the final kilometre with Roenning having the better sprint to clock a winning time of 43:26.0 minutes.
Sundby was another 0.9 seconds further adrift in third while Northug didn't have enough left towards the end as he settled for fourth, 5.5 seconds behind.
However fourth was still good enough for Northug to extend his lead in both the mini tour and the overall World Cup standings ahead of the season-closing 15km freestyle on Sunday.
Northug now leads Vylegzhanin in the mini tour by 30.5 seconds, up from 27.3 after his second successive stage win in the prologue on Friday.
He also extended his advantage over second-placed Alexander Legkov, 15th in the mass start and 16th overall, in the World Cup standings from 56 points to 80 with one event remaining.