The hosts' coach Vincenzo Montella was without leading goalscorer Giuseppe Rossi, who suffered a knee ligament injury in Sunday's Serie A win over Livorno.
However, even without the Italy international, Fiorentina's progression to the next stage of the competition was rarely in doubt thanks to first-half goals from Joaquin and Ante Rebic.
It was Joaquin who had the first attempt of the game, firing over the bar after Mati Fernandez has set up the opportunity, although the winger would get his goal a minute short of the half hour.
The Spaniard struck a drive low past Marco Silvestri in the Chievo goal, before Rebic doubled his side's advantage on the stroke of half-time when he reacted to quickest to Borja Valero's free-kick after it struck the crossbar.
The goals ended there, although the second half was not without controversy, as both sides saw men sent off.
Chievo's Gennaro Sardo was the first to receive his marching orders, picking up a second yellow card for diving in the 68th minute, before Fiorentina veteran Massimo Ambrosini was dismissed six minutes from time.
Again, the former Milan man was shown a second yellow, this time for a late challenge on Perparim Hetemaj, but that was not enough to derail Fiorentina's progression as Montella's men made the last eight for a second successive year.
Fiorentina will now face Catania or Siena in the next round of the competition.
