The American, who won gold in Astana last year, had sat in third place after Saturday's races.
However, she clocked 37.86 seconds in the 500m to win and backed that up with victory in the 1000m, in a time of 1:15.28 minutes to top the pile.
Fellow American Heather Richardson-Bergsma, the 2013 champion who had led the way overnight, was forced to settle for silver while Jorien ter Mors of the Netherlands took bronze after a disappointing eighth-place finish in the 500m.
In the men's competition Pavel Kulizhnikov took his place at the top of the podium, also successfully defending his title after an impressive Sunday.
The 21-year-old won the 500m in 34.63 seconds, ahead of compatriot Ruslan Murashov in second, before clocking 1:09.84 minutes in the 1000m to finish runner-up behind Duthchman Kjeld Nuis.
That earned Nuis the overall silver medal, while his countryman Kai Verbij completed the podium by taking bronze.