Norway had gone 21 individual World Cup events without a victory, but Fannemel beat Germany's Richard Freitag and Poland's Kamil Stoch to the win, his nation's first since Daniel-Andre Tande stood atop the podium in January.
Fannemel jumped 133m in the first round to score 128.7 and top the standings at the half way point, with Japan's Junshiro Kobayashi and compatriot Robert Johansson tied in second on 122.3.
Kobayashi could not produce in the second round, though, as he only scored 119.4 and dropped down to seventh overall, with Fannemel notching 124.9 to total a mark of 253.6.
Stoch clinches victory in Innsbruck
That was good enough to take the win from Freitag by just 0.1 points as the German scored the biggest jump of the second round, but his effort of 131.7 was not quite what he needed.
Freitag does lead the overall World Cup standings, however, with Andreas Wellinger in second, 91 points behind his countryman on 359.
Tande sits third, on 350, with Fannemel down in 11th after recording just his second top ten of the season.
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