Bergsma, 26, posted a time of 12:50.40 minutes to take the win ahead of compatriot Bob de Jong, who was 0.82 seconds off the pace while Seung-Hoon Lee of South Korea was third.
Bergsma had already picked up finishes of second and third this season and he now leads the 5000m standings ahead of compatriot Sven Kramer, who was absent from the competition.
In the overall standings, it's Havard Bokko of Norway who is Bergsma's closest challenger, having come home fourth in Astana, 17.14 seconds behind Bergsma.
In the women's event, Canada's Christine Nesbitt collected her second win of the campaign over 1500m, defeating a Dutch trio who were separated by just 0.02 seconds.
Nesbitt's time of 1:57.18 minutes was good enough for victory while Marrit Leenstra was 0.11 behind with Linda de Vries and Diane Valkenburg close behind.
That victory moves Nesbitt, the 1000m Olympic champion, into first in the season's 1500m rankings while she is up to fourth in the overall standings with Czech Republic's Martina Sablikova and Claudia Pechstein still in joint first place.
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- Christine Nesbitt