Zubkov finished 0.66 seconds ahead of the Swiss team of driver Beat Hefti and brakeman Alex Baumann.
Steven Holcomb of Park City, Utah, and Steven Langton of Melrose, Mass., won the bronze medal, finishing another 0.22 seconds back.
Zubkov's last win in a two-man race was at the 2011 world championships. But on Russian ice, he was dominant, taking a sizable lead into Monday's final two runs and then all but sealing the title with a track record in his third heat.
At 39, Zubkov became the third-oldest pilot to win two-man gold. Holcomb and Langton gave the U.S. its first two-man medal since 1952.