Hufner, the winner of the past five World Cup titles heading into the season, has played second fiddle to German team-mates Natalie Geisenberger and Anke Wischnewski this campaign.
Geisenberger stripped Hufner of her World Cup title with a sixth victory from eight last time out at Lake Placid while Wischnewski and Tatiana Ivanova have claimed the other two wins.
However Hufner showed why she should not be forgotten at the season finale and at the perfect venue with Sochi set to host next year’s Winter Olympic Games.
Hufner beat Geisenberger by the narrowest of margins in Russia, 0.038seconds, before Wischnewski in third a further 0.268 behind and then Ivanova in fourth.
It appeared as if it would be a similar story after the first run with World Cup champion Geisenberger leading Hufner and Wischnewski following a track record of 50.984.
However Hufner, who was just 0.001 behind after run one, had other ideas and was to produce the quickest time second time out, 51.027 to take the win.
Geisenberger was the second fastest in 51.066 for second overall while Wischnewski, despite being fifth after a third first time out, stayed in third place.
Hufner's victory kept her in third place in the overall women's World Cup standings with 561 points with Wischnewski closing the season on 655 and Geisenberger 855.
That ensured that the top three positions in the overall women's World Cup were dominated by Germany for the 12th season running, dating back to 2002.