PAOK was once again unable to score against Qarabag.
A disastrous night for Greek teams in the Europa League on Thursday saw the three of them collect just one point, as Olympiakos drew away from home and Panathinaikos and PAOK suffered home losses.
Olympiakos dropped back to the second spot of its pool after drawing 1-1 at Astana in Kazakhstan.
The hosts led after eight minutes via a Djordje Despotovic goal, but Seba replied 22 minutes later for Olympiakos, that deserved a winner in the second half without getting it.
The Reds now have seven points from four games, two points behind group leader APOEL Nicosia who downed Young Boys 1-0 in Cyprus.
Panathinaikos typically crumbled after the hour mark and lost 3-0 to Standard Liege in Athens while finishing the game with 10 men.
Without meeting the standards of its performance two weeks earlier in Belgium, the Greens hit the woodwork early in the second half via Paul-Jose M’Poku, who later saw the red card.
The Belgians made the most of the depleted Greek side – that had Marcus Berg come off injured in the first half – and scored via Ibrahima Cisse and Ishak Belfodil (twice) leaving the Greeks bottom of their group with just one point.
PAOK was shocked by Qarabag at Toumba as the Azeri team doubled its wins within two weeks, triumphing 1-0.
Former AEK Athens player Michel scored five minutes after coming on as a substitute, with PAOK being unable to equalize in the remaining 21 minutes of the game.
Now PAOK is only left with some mathematical hopes of advancing to the next round, with four points from as many games.