Bayern Munich won the game 4-1 to enhance their push for a tenth straight Bundesliga title while Freiburg's Champions League ambitions took a hit with the defeat.
However, a controversial moment occured in the 85th as Bayern led 3-1 when they messed up a substitution.
Bayern prepared a double substitution but Kingsley Coman remained on the field as his old number 29 was held up instead of the current 11.
The mix-up saw Marcel Sabitzer enter the field of play with Coman still on the pitch and the game continued for 17 seconds before the error was realised, leading to a lengthy delay to sort things out.
Freiburg have decided to take advantage of Bayern's lapse in concentration and appeal for a forfeit win which could revive their top four prospects.
"We are in a dilemma through no fault of our own," read an official club statement. "Freiburg had no part or influence on the events surrounding the process. Nevertheless, the legal and procedural rules of the DFB formally force us to play an active role in order to have the processes legally checked.
"In principle, we have no interest whatsoever in this active role, which has been given to us against our will in terms of procedural technology, and we feel extremely uncomfortable in it.
"Ultimately, it burdens the completely uninvolved club - in this case us - with the responsibility for processing an obvious violation of the rules. Nevertheless, after intensive discussions at different levels and a legal examination, the board of Freiburg [has] decided to appeal against the result of the game."
