The 39-year-old, who has won two Olympic, six World Championship and ten World Cup titles, missed last week's global gathering due to back problems, but returned in style in America.
Zoeggeler, like the rest of the field, was competing in Lake Placid for the first time since 2007 and picked up the 55th individual victory of his career and his fifth at the venue.
He clocked 52.369 seconds on his first run and 52.286 on his second for an overall winning time of 1:44.655 minutes in an Italian clean sweep in America.
Germany have done the same thing in four of the eight World Cup rounds this season with Dominik Fischnaller finishing 0.212 behind for second and David Mair 0.350 shy in total for third.
Felix Loch, who won the world title for the fourth time last week, was forced to withdraw from the Lake Placid event with a finger injury but he is still top of the overall World Cup standings.
He leads David Moller, who was ninth in America, by 63 points with 100 on offer at the ninth and final World Cup round, which also acts as the Olympic test event, in Sochi.
Andi Langenhan is 87 away in third after a 14th in Lake Placid with Zoeggeler fourth another 24 back with Germany securing three of the four World Cup titles at round eight.
Tobias Wendl and Tobais Arlt were officially crowned doubles champions and Natalie Geisenberger the women's and they combined with Ralf Palik to secure the team relay title.
The German team combined to maintain their unbeaten run in this season's World Cup team relay competition with a fifth win that saw them take the overall honour.
However, despite Germany's dominance the margin of victory over second-placed USA was tight, with just 0.107 separating the two nations while Zoeggeler was part of the Italy team that finished third.