With only 2,900 tickets dedicated to away fans, the travelling supporters used their overwhelming numbers to attempt to break into the Emirates Stadium - resulting in the match being postponed an hour.
Arsenal have since announced that they have launched a "full review" following last night's unsavoury scenes, and UEFA have now opened disciplinary proceedings against both clubs involved in the match.
UEFA will deal with the case on September 21, the governing body confirmed in a statement on Friday.
"But I must say our supporters dealt well with the situation as well and there was no aggravation".
"The game has now concluded and the majority of supporters have left the stadium and the surrounding area".
Arsenal manager Arsene Wenger was quite surprised to see such large number of Cologne fans.
"It would be completely unfair [to be punished by UEFA] because I think we prepared well before the game to stop people who are not Arsenal members to buy tickets", Wenger told Sky Sports News.
Sanchez made his second start of the season in an impressive showing, capping his performance with a sublime effort in the second half - his first goal of the season against the Bundesliga's bottom side.
Earlier, YouTube footage showed thousands of Cologne fans surging through the streets of London, chanting and setting off flares. It was clear during the match that many away supporters were sitting among Arsenal fans in the stadium, with some of them causing problems for stewards.
"Many tickets were sold through touts, and this is very disappointing".
Mertesacker, who played the 90 minutes in Arsenal's 3-1 win last night, admits that it was an annoying atmosphere as the players wanted to get on with the game as soon as possible.
Head coach Peter Stoger was asked on the eve of the game if he had a message for the thousands of fans making the trip, to which the Austrian replied: "Enjoy the pubs!"