Mame Diouf's goal and a brace from Didier Ya Konan earned the Reds all three points to leave the visiting players in tears.
Hoffenheim's dramatic win over Borussia Dortmund meant they slipped two places and were relegated after only one season in the top flight following their 12th game in a row without a win.
Hannover coach Mirko Slomka said his side would honour their final game of the season and give the sell-out 42,000 crowd something to cheer, and his team did not let him down.
Although they took a bit of time to get warmed up, as soon as Diouf put them in front after half an hour, there was only ever going to be one winner.
Diouf turned in a cross from Steven Cherundolo, who this week signed a contract extension.
There was no real reaction from Dusseldorf, who showed a degree of nervousness which befitted a side who had not won a game since mid-February.
Ya Konan put the Reds two in front on the hour mark, with Diouf providing the assist this time.
With Hoffenheim at the time losing to Dortmund, Fortuna were nevertheless heading for a relegation play-off, even when Ya Konan netted his second.
However, as the news filtered through that Hoffenheim had drawn level, Dusseldorf knew they were reliant on Dortmund holding on for a point.
But those hopes were dashed as Hoffenheim sealed a 2-1 win, condemning Dusseldorf to relegation and raising questions over the future of their coach Norbert Meier.