Kick-off had to be delayed by an hour after visiting Cologne fans got into the home end at the Emirates.
Police held hundreds of fans behind a cordon outside the stadium while trying to enforce ticket checks, but some supporters burst through and gathered outside the ground.
When the turnstiles were finally opened Cologne supporters who had purchased tickets in the home end from touts were seen jumping barriers to try to reach the away section.
Fans fought with stewards and riot police with dogs were deployed on the edge of the pitch to control the situation.
Arsenal have vowed to get to the root of the problem after the chaotic scenes.
A statement read: "Following last night's UEFA Europa League match with Cologne 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 to prevent tickets being sold to visiting supporters.
"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. We also worked with our colleagues at Cologne to stop supporters travelling without match tickets.
"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."
Arsenal went on to win the game 3-1.
