Tens of fans donning white boiler suits emerged from a section of the ground housing away supporters after Granit Xhaka had netted a stoppage-time winner for the hosts.
Flares were also hurled onto the playing surface during the Bundesliga clash, before the offenders made their way from the pitch as police closed in.
Cologne have since moved to ban the Boyz fan club and withdraw their status as an official supporters' club, and Borussia managing director Stephan Schippers says he will co-operate fully with the German Football Federation (DFB).
"We are part of an ongoing process," he said. "The DFB has asked us to give an opinion on the incidents. We will do that so the DFB can get a full picture of what exactly happened.
"The actions originated from the Cologne fan block. However, we do not want to give the impression that we do not mind the whole incident and that it does not concern us. That would be turning a blind eye.
"We also need to learn the lessons from these events and consider whether and, if so, how the rules might be better in the future."
