The German football federation's (DFB) sporting tribunal said it could find no justification for ordering a replay of the relegation play-off second leg that ended 2-2, giving Fortuna a 4-3 aggregate win.
The club, who went straight down after only season in the top flight, said the decision was "totally incomprehensible" and that they would appeal to the DFB's highest tribunal, the Bundesgericht.
"The appeal was not successful because no reasons for objection could be found," said Hans Lorenz, head of the tribunal.
"The referee at all times acted according to the rules and Hertha's claim that the team was weakened by the interruption could not be proved."
The 2-2 draw in Dusseldorf was interrupted twice for a total of about 30 minutes by a pitch invasion and flares. The game was first stopped after Fortuna scored on the hour to take a 2-1 lead, leaving Hertha needing two goals.
Dozens of lit flares from both groups of fans landed on the pitch, prompting referee Wolfgang Stark to stop play.
The game was interrupted again for more than 20 minutes deep in stoppage time after hundreds of Fortuna fans poured on to the pitch thinking it was over and forcing both teams to seek refuge in the changing rooms.
Hertha said their players were reluctant to return to the pitch and that they were afraid.
"For Hertha, it's totally incomprehensible that a player has to be injured in order for the result of match to be overturned," the club said in a statement.
"It should be sufficient that a game has finished amid completely irregular circumstances and the players as a result of the situation could no longer concentrate on the football match."
