Valencia, Ludogorets Razgrad, Esbjerg, Rubin Kazan and Dnipro Dnipropetrosvk also qualified with two games to spare.
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 percent 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.
(Writing by Brian Homewood in Berne; Editing by Alison Wildey)
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