A statement on the organisation's Facebook page claimed the current situation was "unworkable" and "the values the North Terrace were founded on are no longer reflected in the current culture and environment."
The move comes just hours before Victory face Melbourne City in an FFA Cup semi-final derby on Tuesday night.
"All fans wishing to continue to support within the designated active areas will not be aligned with the North Terrace identity. All materials and leadership will not be present at future matches," the statement said.
Victory responded Tuesday afternoon on their Facebook page saying they were "incredibly disappointed" with the move, insisting they are "fully committed to ensuring our active areas will always be vibrant, safe and enjoyable, creating a unique and inclusive atmosphere."
"To be clear, we will not change our stance of zero tolerance on anti-social behaviour. There is no place for it at our club or in our game," Victory said.
Ten days ago, Football Federation Australia (FFA) reprimanded Victory after a fan lit a flare during the Melbourne Derby at Etihad Stadium.
Fans appeared to be angry at the club's response, with numerous comments criticising Victory's actions in the past.