The Dutchman headed to Russia with just 45 points from his World Cup opener on home ice in Heerenveen.
But he now sits top of the pile after collecting the maximum 100 points in Russia, his time of 10:00.7 enough for victory.
Bergsma is just five points ahead of France's Alex Contin after he finished third, with compatriot Ewen Fernandez just ahead of him in second.
There was more for the Dutch fans to be happy about in Russia as Koen Verweij claimed victory in the men's 1500m.
The victory moves Verweij up to third in the overall rankings, compatriot Maurice Vriend holding on to top spot with 145 points despite finishing sixth.
Completing the podium in Russia were Bart Swings of Belgium in second, with American Brian Hansen in third.
And in the women's 3000m the victory went to Germany's Claudia Pechstein, with Czech Martina Sablikova in second and Dutch skater Marije Joling third.
The victory moves Pechstein up to third in the overall standings on 121 points, Sablikova 39 points ahead in second on the same total as German Stephanie Beckert after she finished fourth in Russia.
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- Ice Skating