0217 GMT November 28, 2020
The German club faces four charges, including crowd disturbances and setting off fireworks while the Gunners face a charge over blocked stairways, BBC reported.
The game was delayed by more than an hour as thousands of away fans arrived at Emirates Stadium without tickets.
About 20,000 Cologne fans turned up in London despite the German club being given a ticket allocation of 2,900.
This case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on September 21.
'I thought they would not play'
Arsenal launched a review and its statement on Friday read, "We 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 kickoff. Many tickets were sold through touts and this is very disappointing."
Arsenal manager Arsene Wenger said he was surprised the match –which his side won 3-1 – was played.
"Do we move it to Tuesday and play Thursday? It was all kind of speculations you know that we had to analyze and see how we can deal with the situation," he said.
"But in the end at some stage I thought they would not play the game, because I can't see the police taking any risk.
"We live in a society of 100 percent security and I thought they would never take a gamble to play this game when I saw the images around the stadium. But I must say our supporters dealt well with the situation as well and there was no aggravation."
Cologne coach Peter Stoger refused to be questioned on the actions of his club's supporters, "I have no comment about the fans," he said.
"I'm the coach, my job is the team, my job is football, not the fans."
Police said five people had been arrested on suspicion of public order offences.