The result secured a 4-3 aggregate play-off win for Fortuna that sent the club from the capital down to the second division.
Fortuna, who won the first leg 2-1 in Berlin last week, returned to the top flight after 15 years.
It was the second relegation in three seasons for Hertha, who had Anis Ben-Hatira sent off early in the second half, leaving Berlin again as the only major European capital without a top-division team.
The result also spells the end of a disappointing return to the Bundesliga for 73-year-old veteran coach Otto Rehhagel, who took over in February with the mission to rescue Hertha.
"We are all bitterly disappointed," said Hertha midfielder Christian Lell. "It is difficult to find words right now."
The hosts got off to a perfect start, stunning Hertha with a first-minute goal from Maximilian Beister's 20-yard strike.
Hertha levelled with a header by Ben-Hatira from a Ronny free kick and missed several chances before the break.
They were reduced to 10 men when Ben-Hatira was dismissed in the 54th minute for a second booking and Ranisav Jovanovic headed in off the post for Fortuna's second goal just before the hour.
The goal sparked a shower of lit flares on to the pitch from both sets of fans and referee Wolfgang Stark stopped play for several minutes.
Needing two goals, Hertha ventured forward and grabbed an equaliser five minutes from time when Raffael unleashed a thunderous shot from just inside the box.
The game was interrupted again for 20 minutes in stoppage time after Fortuna fans poured on to the pitch thinking it was over.
"There was an escalation," German Football League (DFL) refereeing chief Hellmut Krug said. "We can be happy that it did not turn into something more serious."
Eintracht Frankfurt and Greuther Fuerth have already won automatic promotion to the Bundesliga while Kaiserslautern and Cologne were relegated from the Bundesliga.