The Brazilian's set piece at the death rescued the hosts from embarrassment as two goals from two substitutes saw the Serie B side draw level from a two-goal deficit
Efforts from Andre Dias and Tommaso Rocchi saw Edoardo Reja's men go two goals up, but substitutes Emanuele Berrettoni and Marco D'Alessandro drew the Serie B side level in the second half. However, Hernanes had the final say as his free-kick in the 90th minute was curled in to send the home side through to the quarter-finals.
Verona were nearly ahead after only 28 seconds of play, after Sasa Bjelanovic’s header from point blank range was stopped by a stunning one-handed save from Albano Bizzarri.
The home side settled down soon after that early scare, but with Verona content to sit deep and soak up the pressure, they found it difficult to find a meaningful sight on goal.
However, that all changed in the 36th minute, when a swift piece of interplay between Rocchi and Giuseppe Sculli saw the former tee up the latter for a pot-shot which flew about a foot wide.
The hosts went even closer two minutes later after a searching ball by Cristian Ledesma found Rocchi unmarked at the edge of the six-yard box, but the veteran striker’s volley was thwarted by Rafael.
Lazio were finally able to break Verona’s resistance a minute before the interval, when Ledesma’s corner went unchallenged, leaving Dias with the simplest of tap-ins from two yards out.
Reja’s men soon got a second via a fortuitous goal by Rocchi in the 58th minute, when his strike took a huge deflection off Giuseppe Pugliese, looped over Rafael and nestled into the back of the net.
Verona wasted little time in responding. Pugliese made amends for his unfortunate error when his pinpoint cross was headed in from close range by substitute Berrettoni in the 61st minute.
Berrettoni turned provider 12 minutes later, as his incisive ball from midfield released fellow substitute D’Alessandro past the Lazio back line to slot past Bizzarri and incredibly draw the visitors level.
Both sides went on the offensive in a bid to find a winner, and Matteo Abbate blasted into the side-netting from a counterattack before Miroslav Klose spurned two good chances - heading wide from point blank range and volleying over the bar from eight yards out.
There was still a final twist to the drama, and Hernanes curled home a superb set piece from 20 yards out on the stroke of injury time to break the hearts of the Serie B side and send the Stadio Olimpico crowd wild.
Lazio now advance to the quarter finals, and will play the winner of the Milan – Novara tie which takes place at San Siro in eight days’ time.