AEK Athens and Kerkyra were already mathematically assured of relegation to the 2013–14 Football League.
Four teams were promoted from the 2012–13 Football League, champions Apollon Smyrnis, runners-up Ergotelis, third placed AEL Kalloni and Panetolikos, the winners of a four-team play-off round.
Note: Flags indicate national team as has been defined under FIFA eligibility rules.
In the play-off for Champions League, the four qualified teams play each other in a home and away round robin.
Instead, a weighting system applies to the teams' standing at the start of the play-off mini-league.