The 29-year-old three-time World Cup champion powered around the Alberta course and was effectively guaranteed the win in the 10km classic mass start with over 1500m to go.
With World Cup leader Marit Bjoergen absent in order to concentrate on the upcoming Tour de Ski, Kowalczyk stretched the field in the second of three laps, giving herself a sizeable lead going into the final loop.
Kowalczyk, who finished second in the Ruka Triple, recorded a time of 28:58.4minutes to claim her first World Cup win since her 10km classic victory on home soil in Szklarska Poreba back in February.
Anne Kylloenen could not match the Polish skier's pace but did do enough to take second 14.4 seconds behind while Maiken Caspersen Falla took third ahead of four fast-finishing others.
Norwegian Falla had the quickest sprint at the death to deny Vibeke Skofterud, Ingvild Flugstad Oestberg, Kikkan Randall and Kristin Stoermer Steira in that order ending 28.2 behind Kowalczyk.
The win was the 22nd of Kowalczyk's World Cup career and, with the sprint and skiathlon still to come in Canmore, she could yet be topping the podium once again.
"It was a great race. My skis were working perfectly and I like this track," she said. "I don't know what is going to happen in the next races but I will be trying my hardest."
In the men's race Tim Tscharnke timed his break to perfection to claim his first-ever cross-country skiing World Cup victory in the men's 15km classic mass start on his 23rd birthday in Canada.
There was little to separate the front-runners for much of the race in Canmore before birthday boy Tscharnke made his move with 1000m to go for a historic victory.
Tscharnke, who claimed Olympic team sprint silver at Vancouver 2010, had never claimed an individual podium finish let alone a win but that all ended following the final climb.
The German quickly built up a healthy lead that was not to be beaten as he recorded a winning time of 41:14.8minutes in the first of three events for both the men and women Canmore.
Tscharnke was one of three Germans in the top six with Norway's Sjur Roethe finishing second 4.8 seconds behind for second with Tobias Angerer was a further second back for third.
Russian Evgeniy Belov was fourth and Italian Giorgio Di Centa fifth before the third German, Hannes Dotzler, rounded off the top six, 9.3 overall behind Tscharnke.