Kick-off was delayed for an hour after 17,000 fans of the German club arrived in north London without tickets.
UEFA revealed on Friday morning it had opened disciplinary proceedings following the crowd trouble with charges brought against both clubs.
Cologne had been allocated just 3,000 tickets for the game, with many more gathered outside the Emirates preventing home supporters to gain entrance through turnstiles. Arsenal went on to win the Group H clash 3-1.
The Gunners issued a statement on Friday: “We would like to stress that fan safety was always our paramount concern and informed all decisions made.
“We worked in full consultation with police and UEFA officials on the night and in advance of the game and had taken extensive steps in advance of the game to prevent tickets being sold to visiting supporters.
“We also worked with our colleagues at Cologne to stop support traveling without match tickets. This included a number of measures including ensuring no tickets were sold via general sale and that no red memberships purchased after the draw were able to be used to get tickets in the home end for this match.
“The 3,000 tickets issued to Cologne fans was in line with competition rules but it is clear many more visiting fans arrived, causing significant congestion and disturbance outside the stadium before kick-off.
“Many tickets were sold through touts and this is very disappointing.
“We have launched a full review into the circumstances surrounding the game and will ensure any lessons that can be learned are used in the future.”
A police statement issued after the game said: “No reports of any significant incidents. Five people have been arrested on suspicion of public order offences.
“The game has now concluded and the majority of supporters have left the stadium and the surrounding area.”
After the match on Thursday night, Arsene Wenger believed UEFA should take action saying they “are the only master to analyse the facts of what happened”.
Ian Bolton, a senior reporter with Sky Sports News, provided his eye witness account of the incident: “I was told the stadium was in lockdown as a police operation went on outside.
“Inside the stadium it became apparent that Cologne fans were getting into an Arsenal section behind the goal at the south end of the stadium.
“There were scuffles between away fans and stewards as Cologne fans tried to cross a line of stewards to try to get into the adjacent away section.
“Some succeeded in getting through. Others remained in the Arsenal section. Police wearing helmets, and with dogs arrived, and remained in position for the match.
“There were 3000 Cologne fans in the away section, in the South east corner of the stadium, but thousands more had managed to get into the stadium.
“Probably several thousand in the section behind the goal adjacent to the ‘away’ area, and probably several thousand in the upper tier at the same end. There were also smaller groups of away fans in the middle tier.
“There was a line of stewards and police in the stand behind the goal at the southern ‘clock’ end, but there were Cologne fans either side of it!
“At the north end, there were many empty seats. Don’t know if it was because Arsenal fans had decided not to come in the first place, or decided to go home once they got here.”
Cologne said they needed to know more information before issuing a statement, with a club spokeswoman explaining: “We have to first inform ourselves and in the next few days we will talk about that.”