The Armenia international's participation in the match had been in doubt due to the ongoing conflict between Azerbaijan and his native country.
Arsenal had been working with Uefa over securing their player's welfare for the May 29 final.
"We have thoroughly explored all the options for Micki to be part of the squad but after discussing this with Micki and his family we have collectively agreed he will not be in our travelling party," Arsenal said in a statement.
"We have written to Uefa expressing our deep concerns about this situation. Micki has been a key player in our run to the final so this is a big loss for us from a team perspective.
"We're also very sad that a player will miss out on a major European final in circumstances such as this, as it is something that comes along very rarely in a footballer's career."
Mkhitaryan has made 39 appearances for Arsenal in all competitions this season, scoring six goals. The 30-year-old won the Europa League crown with Manchester United in 2017.
"It's the kind of game that doesn't come along very often for us players and I must admit, it hurts me a lot to miss it," he wrote on Instagram.
"I will be cheering my teammates on! Let's bring it home."
Arsenal expressed their disappointment last week over the ticket allocation for the final and urged Uefa to explain its decision to stage the showpiece event in Azerbaijan.
Uefa defended the decision, saying an all-English final was not a predictable event at the time the venue was decided and promised to work with both clubs to assist fans.
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