Kowalczyk, who sat out of the sprint event to nurse a foot injury, made a strong start and clocked the best times at all three intermediate checkpoints to finish in 28 minutes, 17.8 seconds.
Swede Charlotte Kalla took silver, 18.4 seconds behind, and Norwegian Therese Johaug won the bronze after finishing 28.3 seconds off the pace.
Pre-race favourite Marit Bjoergen of Norway came fifth after fading towards the end of the race, held in bright sunshine with temperatures reaching 13°C.
"It's the first time of my life that I race in such warm weather," Russian Natalia Zhukova, who finished seventh, told reporters.
It was Kowalczyk's fifth Olympic medal and her second title after she won the 30km classic race in Vancouver.
Her chances of shining at the Sochi Games had taken a hit when she suffered a micro fracture in her left foot two days before the opening event.
However, the four-times overall World Cup winner started last Saturday's skiathlon and finished sixth before deciding to give the sprint a miss.
It paid off on Thursday as she never looked in danger, opening a healthy 9.1-second lead at the halfway mark.
Kalla, who won the 10km freestyle at the Vancouver Games, collected her second silver medal in Sochi, making a cautious start before finishing strongly.
World Cup leader Johaug, who finished fourth in the skiathlon, won her first medal of the Games by edging out Finn Aino-Kaisa Saarinen by two seconds.