The two-time PyeongChang medallist sealed top spot to cross the line in 6:16.168, over three seconds ahead of Russian rival Alexander Rumyantsev.
Canadian Ted-Jan Bloemen scooped third as Pedersen moved to the top of the overall World Cup standings and ahead of Rumyantsev by just one point.
In the 5000m Men's Division B, Canadian Graeme Fish recoded a personal best time of 6:23.387 to take top spot.
Elsewhere, three-time Olympic champion Czech Republic skater Martina Sáblíková showed no nerves to clinch the 3000m Ladies Division A gold.
The 31-year-old claimed the full 60-point prize to add to her World Cup overall lead by rocketing across the line in 4:02.177.
Russian Natalia Voronina scooped silver, while Belarus' Maryna Zuyeva took bronze.
And Netherlands' Joy Beune took gold in the 3000m Ladies Division B.