Although the Umbrian outfit are struggling in Serie A, they recovered from a 2-1 first leg deficit to seal a morale-boosting 4-2 aggregate success.
Chris Obodo headed the opener just before half time to break the deadlock.
Souleymane Diamoutene pounced to double the lead after Zisis Vryzas had been thwarted by Giorgio Frezzolini in the Chievo goal.
Jay Bothroyd (pictured) put the seal on an impressive win with the third strike to assure Perugia of a place in the next round.
