Cologne have been charged with four offences at the match which was delayed by an hour after large numbers of German fans descended on the Emirates Stadium, the majority of them without tickets.
Arsenal face a charge relating to the blocking of a stairway in the away fans sector.
However, UEFA's Control, Ethics and Disciplinary Body (CEDB) said the inspector would now "initiate the appropriate disciplinary investigations".
"The Ethics and Disciplinary Inspector will contact both clubs in order to evaluate the scope of their respective responsibility as regards the incidents connected to this match," UEFA said.
Russian club Spartak Moscow have been fined 60,000 euros (£53,085) and will be banned from selling tickets to supporters for their next away match in Europe, at Sevilla on Nov. 1, following the throwing of objects and setting off of fireworks during their Champions League game in Slovenia against NK Maribor.
Sevilla head coach Eduardo Berizzo will serve a one match ban after he was sent off during the Champions League match against Liverpool on Sept. 13.
Croatian club Hajduk Split have been fined 40,000 euros after misbehaviour from their fans at Everton in a Europa League playoff match in August.
Split have also been ordered to settle with Everton the cost of damages caused by their fans at Goodison Park. The English club were fined 10,000 euros due to their fans throwing objects at the same game.
(Reporting by Simon Evans; Editing by Christian Radnedge)
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