The away side showed their quality early on with the majority of possession. Oleksandr Yakovenko and Marcos Alonso combined out wide, but the former's cross was cleared. Alberto Aquilani then charged into the final third as La Viola pushed for an early goal.
Ryder Matos then volleyed tamely towards goal as Pandurii struggled to get out of their own half. The best they could muster in the opening 17 minutes was a cross from David Distefano that ran out of play.
Their first effort on goal saw Alin Buleica drag a shot wide from just outside the area.
However, the Romanian outfit then stunned their opponents by opening the scoring. Eric Pereira connected with Buleica's cross and volleyed in on the turn.
Pereira was almost in on goal again as Pandurii pushed for a second, but Fiorentina managed to clear.
Borja Valero wasted La Viola's best chance of the match up until that point, hitting a shot wide from eight yards.
Alex smashed over a long-range shot for the hosts, but they could not hold on for the win as Matos pounced from close range to equalise.
There was more heartbreak for the home side, however, as Valero struck in the 92nd minute to send La Viola through to the knockout stages.