Russian pilot Zubkov started the season in a rich vein of form in the four-man, winning the opening four rounds in Lake Placid, Park City, Whistler and Winterberg.
However, second in La Plagne and the decision to miss the Altenberg round, saw Zubkov fall to second in the overall World Cup rankings behind Germany's Maximilian Arndt.
But back on the ice in Koenigssee, Zubkov led from start to finish to win by 0.20seconds ahead of German No.1 pilot Arndt and German No.3 pilot Thomas Florschuetz.
Zubkov posted 48.91 to sit top after the first run with Arndt just 0.06 away in second with Florschuetz third before the third German crew driven by Manuel Machata in fourth.
The Russian then posted the quickest time of the second runs, 49.15, for an overall time of 1:38.06minutes with Arndt just managing to hold onto the runners-up spot.
He went slower than Florschuetz, Machata and Oskars Melbardis second time out in 49.29 but took second by 0.10 and 0.17 ahead of his German teammates respectively.
Ardnt held a 39-point lead over Zubkov ahead of round seven in Koenigssee, which also marked the start of the Triple Trophy, but that advantage is now down to 14.
Meanwhile Britain's John Jackson and his crew were ranked outside the top ten after a first run of 49.52 but broke into it after going 0.17 quicker on run two.
Once again he was joined by Lamin Deen on the ice in Koenigssee but, like the two-man event, he couldn't do enough to earn a second run, his crew ranking 23rd after clocking 49.96 first time out.