Arsenal feared political tensions between the midfielder’s native country and the host nation would rule him out of their trip to Baku
Armenia and Azerbaijan have been in conflict over issues in the disputed Nagorno-Karabakh region for three decades.
And Arsenal feared Mkhitaryan, 30, could fall victim to difficult diplomatic relations between the two nations.
The Armenian midfielder was at risk of failing to obtain a visa, which would rule him out of the Europa League final on May 29.
But Azerbaijan’s foreign ministry spokeswoman Leyla Abdullayeva insists politics will not stand in his way of helping the Gunners claim the title.
She said: “Many major sports events have been hosted in Azerbaijan, and Armenian athletes have taken part in them. Sports and politics are separate.”
But Arsenal still demand assurances from Uefa over Mkhitaryan’s safety in Baku.
The Gunners ace has already pulled out of two games played in Azerbaijan in the past.