The striker who was sent off in his last game for the Sky Blues had four efforts but could do nothing as Gekas hit a hat-trick and the tally was added to by Basinas and Amantidis to send Greece to the top of Group C.
Mifsud on international duty
Former Sky Blues Robbie Keane scored for Ireland in a 2-2 draw with Wales. Lee Carsley also played.
England's chances of qualification improved when Israel beat Russia but Scotland are out after a 2-1 home defeat by Italy.
Northern Ireland still have a slim chance of qualification after a 2-1 win against Denmark. David Healy hit the winner after a Warren Feeney goal had cancelled out one from Nicklas Bendtner. It was the one time City target's 13th goal in the competition and set a new record.