The Netherlands' Renate Groenewold clinched the silver medal in a thrilling final race, during which she threatened Pechstein's new mark of three minutes 57.70 seconds, at one stage.
Cindy Klassen of Canada, who competed in Pechstein's race, took the bronze.
Pechstein broke her own world record of 3:59.26 in the penultimate duel of the competition.
Klassen also broke Pechstein's old record in that race and must have thought that she was assured of the silver - that was until Groenewold began to threaten the new world mark.
The German became the second skater to break a world record in two days following Jochem Uyldehaage new mark in the men's 5,000m on Saturday.
"I have earned my medal, I am very happy," she said. "I was lucky to be paired with Cindy, I think it was a dream team."
It is believed that the fast times are due to fact that the track is the highest covered oval in the world, resulting in less air drag and bonehard ice.