Apollon suffered a 2-1 defeat against Italian side SS Lazio away from home in Group J on Thursday night, and they now remain in third position with four points.
The Italians are in second place with eight points, two points behind group leaders Trabzonspor who beat Legia 2-0 in Warszawa on the night.
Sergio Floccari’s first half brace put Lazio 2-0 ahead, but Apollon’s Greek midfielder Fotios Papoulis set up the final score six minutes before the interval. In three weeks’ time the Cypriot cup holders travel to Turkey to face Trabzonspor.
Elsewhere in Europa on Thursday, Fiorentina fell behind to a spectacular scissors-kick goal from Pandurii’s Eric Pereira before hitting back in the last five minutes to win 2-1 and lead a charge of teams into the knockout stages.
Pereira’s fellow Brazilian Alan also scored a stylish goal to help FC Salzburg qualify with a 3-1 win at Standard Liege.
Valencia, Ludogorets Razgrad, Esbjerg, Rubin Kazan, Dnipro Dnipropetrosvk and Tottenham Hotspur also qualified with two games to spare.
There were shock wins for Maccabi Tel Aviv, who beat Eintracht Frankfurt 4-2, and APOEL, who beat Girondins de Bordeaux 2-1.
Pandurii stunned Fiorentina when Pereira met a cross from the left with a scissors kick and scored with a shot which looped into the top corner from just inside the penalty area.
The Romanians were four minutes from a shock win in Group E until Juan Cuadrado broke down the right and rolled a low ball across for Brazilian Ryder Matos to tap home. Cuadrado then teed up Borja Valero to volley a stoppage-time winner.
Dnipro’s 2-0 win over Portuguese side Pacos Ferreira also sent them through, wrapping up the group with two rounds of matches to play.
Group C was also concluded prematurely when Salzburg progressed alongside Esbjerg, who beat Elfsborg 1-0.
Alan, the subject of discussions about a possible naturalisation and call up for Austria, capped Salzburg’s win in Liege when he brilliantly volleyed in Valon Berisha’s cross just before the hour.
Pablo Piatti scored twice to give Valencia a 3-2 win at St Gallen which sent the Spaniards through from Group A despite Jonas missing a second-half penalty.
Ludogorets qualified from Group B despite losing their 100 per cent record in a 1-1 draw with Chornomorets Odesa and Rubin Kazan’s 1-0 win over English second-tier side Wigan Athletic sent them through from Group D.
Erik Lamela and Jermain Defoe, from a penalty, scored in a seven-minute second-half spell to give Tottenham a 2-1 win at home to Sheriff Tiraspol in Group K, their fourth straight win.
Ismail Isa pulled one back for the Moldovans, the first goal that Tottenham have conceded in the group.