The match had to be stopped twice, the second because of a pitch invasion, but eventually the visitors were relegated to the second division after going down 4-3 on aggregate.
Maximilian Beister gave Fortuna a dream start with a goal inside the first minute, but Anis Ben-Hatira replied with a header in the 22nd minute.
Ben-Hatira was given his marching orders for a second yellow card in the 54th minute and Fortuna did not need long to take advantage with Ranisav Jovanovic putting them 2-1 up five minutes later.
Hertha fans manifested their frustration, interrupting the play as they threw fireworks onto the pitch, and not even an equaliser from Raffael in the 84th minute could appease them as they again disrupted the proceedings, causing seven minutes of stoppage time to be added.
A pitch invasion with a minute still to be played caused a further delay before referee Wolfgang Stark blew the final whistle to bring an end to the drama and seal Fortuna's return to the top flight.
Beister, who will join Hamburg next season and was therefore already certain of a place in the Bundesliga, gave the home side a perfect start with a long-range effort which caught Thomas Kraft cold with less than a minute played.
Hertha responded well and deservedly levelled through Ben-Hatira in the 22nd minute as he headed Ronny's free-kick past Michael Ratajczak.
Hertha's chances of getting the goal which would have levelled the tie were dealt a blow when Ben-Hatira was sent off for a second yellow card in the 54th minute.
Five minutes later, Jovanovic headed Fortuna back in front from Thomas Broker's cross, but the drama was only just beginning.
Adam Matuschyk shot wide of an open goal as he missed the chance to seal Fortuna's return to the top flight, and almost in the next Hertha attack, Otto Rehhagel's side levelled.
Raffael played the ball to the feet of Adrian Ramos inside the penalty area, and he returned the gesture to set up Raffael to give Hertha hope with the equaliser on the night.
Only one goal was now needed to keep Hertha in the top flight, but their fans did not seem to care as they once again threatened to force the game's abandonment as they threw more fireworks onto the pitch.
After a break of several minutes the game restarted with seven minutes of stoppage time announced.
With Dusseldorf fans lining the pitch preparing to invade it at the final whistle, Jovanovic missed the chance to seal the win in the sixth minute of stoppage time when he wasted a one-on-one against Kraft.
Hundreds of fans stormed on to the field of play with one minute of the game still to be played.
The teams were forced to leave the pitch as stewards and police tried to send the fans back into the stands, forcing a delay of 15 minutes while order was restored.
Both sides eventually emerged with Hertha seeming reluctant to return to play out the remaining 60 seconds before another pitch invasion greeted the final whistle, with Dusseldorf returning to the Bundesliga in dramatic circumstances.