UEFA have decided to open disciplinary proceedings against Bayern after supporters threw fake money onto the pitch during the match.
The case will be heard by its ethics and disciplinary body on Dec. 7.
Bayern fans were charged €100 for their allocated tickets, and their protest led to play briefly being delayed.
But Heynckes told a news conference ahead of the weekend match at Borussia Monchengladbach: "What are they paying, €100? I totally support the protest — the fans are absolutely right, it is justified.
"It is crazy — the fans cannot afford this. It is practically an invitation to stay at home. It is not OK.