The Greek giants have dropped out of the top flight for the first time in their history, though a points deduction which they are appealing looked to dump them down regardless
Many of the capital club's players broke down in tears upon the final whistle as the Greek giants were condemned to the second tier for the first time in their 89-year history.
The club had already been deducted three points last week, which looked set to relegate AEK regardless of the result on Sunday though an appeal had prevented the decision becoming official.
That point deduction came after an incident in which fans of AEK chased Panthrakikos players after their side had gone behind late in the game, leading to the game being abandoned shortly after the incident and the opposing club were awarded a 3-0 victory by virtue of default.
The club denounced the point deduction, branding the punishment a "premeditated crime" imposed by a "corrupt system".
If the appeal fails AEK will begin their first stint in the second tier of Greek football on minus two points.
Temporary coach Traianos Dellas, who won Euro 2004 as a player with Greece nine years ago, said that he asked for the league to treat his side fairly before the decision was announced.
"What I asked from the committee was for fair treatment," he said. "Matches should end inside the football ground not in court."