Polesitter Leclerc defied expectation by running a two-stop strategy but his late push on fresh tyres failed to produce enough pace to reel in the champion as Verstappen rose from seventh.
Verstappen kept climbing in the early stages of the 53-lap 100th anniversary race at Monza. He relegated AlphaTauri pilot Pierre Gasly for fourth at the end of lap one before diving past 2021 Italian GP winner Daniel Ricciardo under braking into the first chicane for a provisional podium.
That left only Leclerc and second-starting George Russell up ahead, the Mercedes holding firm after aborting the first chicane while squabbling with the Ferrari for the early lead.
Despite the W13 separating the pair, Leclerc and Verstappen traded early fastest laps over the timing line as a net 2.5s split the protagonists.
Formula E champion Nyck de Vries equalled Williams’ best result of the season in ninth to cap off his fine substitute appearance for an appendicitis-side-lined Alex Albon.
Zhou Guanyu, meanwhile, completed the top 10 for Alfa Romeo ahead of Esteban Ocon and Mick Schumacher.
Behind Bottas and Tsunoda, Nicholas Latifi and Kevin Magnussen (picking up a 5s penalty for aborting the first chicane) completed the runners.
Alongside Ricciardo and Vettel, Lance Stroll and Alonso (suspected water pump failure) were forced to pull up early.
