Eric Pereira scored to put the home side in front in the 31st minute but late goals from Matos Ryder and Borja Valero handed the Italians their fourth win in Group E.
The win has moved the Viola to 12 points in the standings, three clear of nearest rivals Dnipro with two games remaining.
Pandurii, meanwhile, have no chance of qualifying as they lie third with one point.
The hosts suffered a setback midway through the first half when goalkeeper Razvan Stanca had to leave with an injury.
He was replaced by Joao Pedro Mingote.
Fiorentina wasted a good chance to break the deadlock before the half-hour mark when Joaquin surged inside the area and struck the ball straight into the body of Mingote.
Pandurii did not waste their opportunity shortly after when Marko Momcilovic's cross found Pereira in the box and his left-footed strike beat Fiorentina goalkeeper Gustavo Munua.
Fiorentina twice had chances to equalise after the re-start but Juan Cuadrado's header flew wide while minutes later, Alberto Aquilani's left-footed attempt went just over the bar.
Pandurii almost doubled their lead on the hour mark when Paul Anton's stinging drive forced Munua into a full-stretch save.
Fiorentina grew in confidence and drew level when Cuadrado fed Ryder in the box and his close-range shot beat Mingote.
With seconds remaining, Cuadrado spotted Valero in the area and his diagonal attempt hit the far post before finding the back of the net.