PAS thought they had earned Greece's final spot in the Europa League - the first time the club had secured a place in Europe in their history - following their fourth-place finish in the top-flight playoffs last season.
The UEFA decision, however, means that PAS will now be replaced in the competition by Skoda Xanthi, the next best-placed club who meet the body's requirements.
"PAS Giannina considers this decision unjust, as well as the fact that there is no information as yet about the reasoning and we will immediately appeal to the CAS," the club said in a statement on Friday.
"The club proved on the field, through its ethos and spirit, that it deservedly secured its European involvement, however, some people managed to deny the joy of thousands of fans using paperwork.
"This unacceptable decision will not break the determination of the PAS Giannina family and that we will continue to battle on the field with honesty and consistency as we always have done."
Panathinaikos, who did not qualify for Europe but were anticipating UEFA's decision concerning PAS Giannina, were hoping that they might sneak into the Europa League as the next best-placed team.
But the Greens announced on Thursday that they had also been denied by UEFA for similar reasons. Panathinaikos said they would also appeal to CAS.
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