The tribunal upheld a May 21 court decision that ruled there was no reason to replay the second leg that saw Fortuna triumph 4-3 on aggregate to gain promotion to the Bundesliga, sending the Berlin club down for the second time in three seasons.
The return leg in Dusseldorf, which finished 2-2, was interrupted twice for a total of about 30 minutes by a pitch invasion and flares.
"The reason for the appeal that argued the Berlin club was weakened due to the incidents towards the end of the game could not be confirmed by the evidence," said the DFB federal court's presiding judge Goetz Eilers after a marathon 10-hour hearing.
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 the game was over and forcing both teams to seek refuge in the changing rooms.
The Berlin club has not yet decided whether it will take the issue further.
"We are disappointed with the verdict," said Hertha president Werner Gegenbauer. "But we will not decide tonight what we will do now."
Hertha had said their players were afraid to return to the pitch and their decision to continue playing was only taken so as not to escalate the situation.
