Gertha Smit of the Netherlands took silver and Clara Hughes of Canada bronze.
Pechstein finished in a time of 6 minutes 46.91 seconds, 2.31 secs inside the mark of Smit, who had broken the old record just an hour earlier.
Coming into the Olympics, Gunda Niemann-Stirnemann of Germany held the record of 6:52.44, which she set at the Utah Olympic oval last year.
The German veteran was not competing because of pregnancy.
"I did't have any doubts because Anni (Freisinger) was better all the
time. I was focusing on the Olympic Games and it worked out
pretty well. "
Double gold medallist Claudia Pechstein
Pechstein had already won the 3,000m in a world record time last week.
Her main rival was compatriot Anni Friesinger who faded to sixth.
The pair have often had a frosty relationship, but Pechstein paused to hug Friesinger on her victory lap.
Friesinger repaid the kindness in her words afterwards.
"Claudia skated an amazing race with an amazing technique," she said.
Friesinger, the gold medalist in the 1,500m, had won all five 5,000m World Cup races this season, with Pechstein finishing second in four of those.
"I didn't have any doubts because Anni was better all the time. I was focusing on the Olympic Games and it worked out pretty well," Pechstein said.