Nuremberg's 3-1 away win at Frankfurt on Saturday was stopped for 20 minutes after some of the visiting fans threw flares onto the pitch.
The match referee sent both teams to the dressing room while police tried to restore order in the stands.
Nuremberg has been warned that any kind of repeat could lead to further matches being played behind closed doors.
"Nuremberg did not take the proper measures in order to protect match officials and the opposing team's players from their unruly supporters," the DFB said Thursday.
Frankfurt was been handed a fine of €25,000 for the actions of its fans.
Nuremberg's win lifted them off the foot of the table, but they remain in second-last spot in 17th. Frankfurt sit in eighth position.