Uncertainty regarding the 30-year-old’s involvement in the showpiece event has lingered for some time.
Political tensions between his homeland and Azerbaijan have led to doubts being cast over his safety.
Assurances had been offered by the UK ambassador of the Europa League final host nation, but not enough has been done to convince Arsenal and the player that he should make the trip to Baku.
A statement from Gunners on their official website read: “We are very disappointed to announce that Henrikh Mkhitaryan will not be travelling with the squad for our Uefa Europa League final against Chelsea.
“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.
“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.
“Micki will continue to be part of our preparations until we depart for Baku at the weekend.”
Mkhitaryan has already sat out one visit to Azerbaijan this season.
He was left out of the Arsenal squad which faced Qarabag in the Europa League group stage.
At that point, the Gunners knew that they may be left with another tough decision to make.
They were a long way from a final berth, but always intended to put themselves in contention for major silverware.
Unai Emery’s side will now be pursuing a continental honour when they face domestic rivals Chelsea on May 29.
They will take on that challenge without Mkhitaryan, but can use his enforced absence as added motivation when taking on their London neighbours.