On his return from a hamstring problem, Dybala shrugged off the attentions of Marco Parolo to tuck home in stoppage time and make sure the Bianconeri remain right on the coattails of Napoli in a two-horse race for the title.
The much-anticipated battle between third and second in the table seemed set to end in stalemate, with both teams cancelling each other out in a disappointing game devoid of clear-cut opportunities.
Juve had a first-half goal correctly ruled out for a foul - sparing Jordan Lukaku the embarrassment of scoring in his own net - as they seemed set to draw a blank ahead of Wednesday's Champions League tie with Tottenham.
Both sides faded in the second half, hardly a surprise after playing in the Coppa Italia in midweek, before Dybala struck right at the death.
The forward converted Daniele Rugani's pass as he fell to the ground to secure three valuable points and make sure Juventus will head to Wembley on a winning note.
The last-gasp strike settled a heavyweight clash that had seen the competitors struggle to land a meaningful blow between them.
The two teams went toe-to-toe after contrasting results in the cup in midweek. While Juventus reached a fourth successive final thanks to a 1-0 victory over Atalanta in the second leg of their semi-final, Lazio lost out to AC Milan in a penalty shoot-out.
Sergej Milinkovic-Savic – one of those who missed from the spot in midweek – had a firm header saved by Gianluigi Buffon in the first half, with the veteran goalkeeper also required to tip a low drive from Ciro Immobile around his right post before the break.
Juventus thought they'd gone ahead when Lukaku nodded Dybala's corner into his own goal just before the half-hour mark, only for referee Luca Banti to correctly spot a push by Mario Mandzukic on the defender.
The official had decided against whistling for a foul in the opening minutes of the second half in the same penalty area, rejecting appeals for a penalty when Dybala theatrically fell under pressure from Lucas Leiva.
The pace dropped significantly after the interval, and Allegri's decision to send on the attack-minded Douglas Costa – resulting in a switch to a flat-back four – still failed to inspire Juventus.
Yet the champions still found a way to triumph before the final bell, Argentine Dybala demonstrating both skill and strength to land the knockout blow in the closing seconds of an otherwise forgettable contest.