The Italian has four World Cup victories on the Norwegian track and clocked up an overall time of 1:38.59, just 0.096 clear of Russian slider Roman Repilov.
Repilov had been sitting in ninth place after a poor first run of 49.419 but a magnificent slide of 49.267 propelled him to second.
Austria's World Champion Wolfgang Kindl finished third with an overall time of 1:38.722.
Loch prevails in Innsbruck but targets World Cup improvement
But this was Fischnaller's day and the 24-year-old, who received treatment from the German team doctor after a back injury, admitted he loves sliding down the Lillehammer track.
He said: "Lillehammer feels like my home track because we train here so much. In my three races on this track I've won twice and come third once. I have to thank the German team doctor who did an amazing job sorting out my back problems."
Kindl was delighted with his spot on the podium and was also happy to see Fischnaller back amongst the medals.
Image credit: Getty Images
He said: "I'm always happy with a podium finish. The competition was really strong. After a lean spell, Dominik Fischnaller is back at the sharp end.
"After training, I thought I might finish even further up but the other guys don't make things easy. Mind you, that's what makes it so exciting."
Felix Loch, who finished fifth in Lillehammer, retains his lead in the overall World Cup standings with 726 points.
Second is held by Kindl (638) and third by Russia's Semen Pavlichenko (547), who had to settle for 15th after a botched first run in Norway.
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