Granerud jumped 140.0m and 138.0m to score his first victory since taking five World Cup competitions in succession earlier in the season, before the start of the Four Hills Tournament.
Kobayashi Ryoyu took seventh place with fellow Japanese Sato Yukiya eighth.
Kamil Stoch's hopes of a fourth consecutive World Cup win were dashed by a disappointing first-round effort of 123.5m which saw him only just make the top-30 cutoff.
The recent Four Hills winner and three-time Olympic champion improved to 131.0m in round two and ended up in 17th place.
Granerud was the hot favourite for the Four Hills but had to settle for fourth behind a resurgent Stoch.
He was second to the Pole on Saturday, and showed he meant business in round one, scoring 151.6 points to leave himself 4.9 points clear of Tande with Eisenbichler just 0.3 further back.
The German was just below par with his second jump, allowing Kraft to move above him, but Tande produced an excellent leap of 138.0m to put the pressure on his compatriot.
And the 24-year-old from Oslo responded, matching Tande's distance to secure his sixth win of the season.
He told FIS afterwards, "I wanted to win, of course. I always want to win. It's been five competitions without a win after five wins in a row so, yeah, it feels great to win again.
"It was tough conditions. It's always a bit strange when you jump in quite a lot of tailwind. You don't get the same answers from the jump or the skis, so you have to be patient in the flying phase and just wait and wait and wait and then put the telemark down. It was a tough day but the hill and everything is so perfect so it was great fun."
Granerud has extended his overall World Cup lead over Eisenbichler to 264 points with Stoch a further 62 points back.
Next up is the large hill in Zakopane, Poland with the team event on Saturday (16 January) preceding Sunday's individual competition.