Joaquin put the Italians ahead in the 26th minute before Matos Santos Ryder doubled his team's lead before the break.
Substitute Juan Guillermo Cuadrado capped a wonderful evening for the hosts with a third goal in the 69th minute.
The result at the Artemio Franchi stadium was Fiorentina's third straight success in the competition and lifted them three points clear of Dnipro, who won 2-0 at Pacos Ferreira in the other pool game.
Pandurii, meanwhile, have dropped to the foot of the standings with the Romanians having mustered one point from three games.
Fiorentina coach Vincenzo Montella rested the team's top scorer Giuseppe Rossi and started with Oleksandr Yakovenko and Matos in attack.
The Romanians had an early chance after just three minutes when Eric Pereira fired over the bar from 20 yards.
Shortly after, Fiorentina goalkeeper Norberto Neto was forced to fully stretch to clear Bogdan Ungurusan's stinging drive from the edge of the area.
Despite Pandurii's early efforts, it was Fiorentina that took the lead when Joaquin got past two defenders and his cleanly struck right-footed shot beat visiting goalkeeper Razvan Stanca.
The Viola doubled their lead in the 34th minute when Matos raced onto the ball in the area and rounded Stanca before firing a right-footed shot into the far corner.
Fiorentina continued to press forward after the break and were rewarded when Yakovenko fed Cuadrado in the box and his 12-yard effort beat Stanca.
Yakovenko was unlucky not get on the scoresheet shortly after when his header from substitute Alberto Aquilani's cross hit the crossbar.
With 11 minutes remaining, Neto did well to keep out Pereira's goal-bound attempt as Fiorentina kept a clean sheet for the second time in the competition.