Due to poor weather conditions the men's singles event was cancelled and later restarted with only one World Cup run.
But Eissler wasn't complaining as the 20-year-old German outshone his peers to take victory as he came home in 52.938 seconds.
Two-time Olympic champion Armin Zoeggeler of Italy had to settle for second 0.044 further back, although the six-time world champion did have something to cheer about as it was his 100th podium World Cup finish of his career.
And completing the podium was German David Moeller as the two-time world champion came home in 52.994, just pipping compatriot Felix Loch to a medal.
Fellow German Johannes Ludwig also had something to shout about as although he finished 17th he set a new start record of 3.789 en route – but there was no denying who the star of the show was in Winterberg.
"I still can't believe it," Eissler said. "Of course it's also due to the fact that I was among the first starters on the track.
"And then the weather conditions also played a role. But anyway, I still have problems to really understand it. I don't think about the Olympic Games at all."
In the overall standings Moeller leads the way on 240 points, ten ahead of Loch with Italian Dominik Fischnaller third on 225.
In the doubles event, Germans Tobias Wendl and Tobias Arlt recorded their second win of the season as they finished in 1:27.491 minutes.
Defending champions Christian Oberstolz and Patrick Gruber of Italy had to settle for second place while Peter Penz and Georg Fischler of Austria and Ludwig Rieder and Patrick Rastner of Italy were tied on third place.
Wendl and Arlt's 19th career victory means they lead the World Cup standings on 285 points, 80 ahead of Oberstolz and Gruber and Germans Toni Eggert and Sascha Benecken.