Berlin, whose final-day Bundesliga victory over Hoffenheim saw them handed a reprieve at the expense of Cologne, went ahead thanks to Czech Republic defender Roman Hubnik’s 19th-minute header.
Fortuna, who finished third in the second division, rallied in the second half thanks to a fine strike from Thomas Broeker and an own-goal from Berlin defender Adrian Ramos.
Dusseldorf last played in the top flight 15 years ago and were playing in the semi-professional regional leagues as recently as 2003.
Berlin, meanwhile, were promoted back to the Bundesliga as second division champions but struggled for much of this campaign, hiring Otto Rehhagel to save their season.
Germany operates a play-off system between the third-bottom team in the top flight and the third-placed side in the second division. The winner over two legs gets to play in the Bundesliga.
Greuther Fuerth and Eintracht Frankfurt have already secured promotion, while Cologne joined long-relegated Kaiserslautern in relegation.