Following Granit Xhaka's late winner at Borussia-Park, sections of the away support entered the field wearing boiler suits with smoke bombs and flares also thrown from the crowd.
Cologne - who are likely to face sanctions from the DFB - stated that Saturday's scenes "intentionally damaged the club".
The Bundesliga club also confirmed members of the group would be denied access to home and away games as well as potentially being liable to further sanctions in future.
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