Verstappen set the benchmark pace on medium rubber in the opening stages before improving on his switch to softs, heading Leclerc by 0.347 seconds in a scrappy session for the Ferraris.
At Williams, appendicitis forced Albon onto the sidelines and one-time Formula E champion de Vries into his seat for the remainder of the Italian GP.
De Vries, who drove for Aston Martin in FP1 in place of Sebastian Vettel, took to the Monza circuit ahead of his race debut on Sunday with 36 minutes remaining of the hour-long session and immediately went 18th on medium tires.
A slow start to the final practice of the Monza weekend meant just six drivers had registered lap times after the first 10 minutes of running.
Red Bull’s Sergio Perez set the early benchmark with a 1m23.448s on medium rubber.
He subsequently improved to a 1m22.611s and a 1m22.148s, with Alfa Romeo’s Valtteri Bottas around two seconds adrift in second after an initial run on soft rubber.
Perez’s Red Bull teammate Verstappen was forced to abort his first flying lap on medium tires just over 10 minutes into the session when he encountered slow traffic in the form of Mercedes’ George Russell.
Several drivers would come across slow-moving traffic on their push laps, with Bottas almost rear-ending the Ferrari of a touring Carlos Sainz into Turn 1 20 minutes in.
Bottas was forced to run through the first chicane having flat-spotted his soft tires trying to avoid Perez, with the stewards placing the incident under investigation before electing to summon the Spaniard after FP3.
Sainz’s session was thrown another complication when he was told to box soon after with a suspected fuel system issue, though was able to get back out on track with around half an hour remaining.
After his initial time attack lap was hampered by Russell, Verstappen shot to the top of the order with a 1m21.872s on medium tires just under 20 minutes into the session as the Ferrari’s of Leclerc moved up to second on the same compound.
Verstappen’s position remained intact when Sainz moved up to second on soft rubber with 15 minutes remaining before the Red Bull driver produced a 1m21.252s on his qualifying simulation on the red-walled tire.
This would stand as the best lap of the weekend so far heading into qualifying, with Leclerc holding second from Perez.
Leclerc locked up on his first flying lap on soft tires towards the end of FP3, taking the best out of the compound for his second attempt.
Sainz ended the session fourth ahead of the Alpine of Fernando Alonso and McLaren’s Lando Norris.
Russell was the fastest of the Mercedes drivers in seventh from Yuki Tsunoda in the AlphaTauri and Alpine’s Esteban Ocon, who joins the list of nine facing grid penalties for Sunday’s race.
Lewis Hamilton rounded out the top 10 in the sister Mercedes ahead of Alfa Romeo’s Zhou Guanyu, Pierre Gasly (AlphaTauri) and the Williams duo of Nicholas Latifi and de Vries.
De Vries improved to a 1m22.869s, though did suffer an off-track moment exiting the first Lesmo with around half an hour of the session still to run.
McLaren’s Daniel Ricciardo headed Bottas, Aston Martin’s Sebastian Vettel, Haas duo Kevin Magnussen and Mick Schumacher – who was kept in his garage until the final 10 minutes due to a clutch issue – and Lance Stroll in the second Aston.