Alfa Romeo’s Kimi Raikkonen and Racing Point’s Sergio Perez crashed in the wet conditions early on, before the drivers switched to dry-weather slicks late on.
Leclerc, fresh from his maiden victory in Belgium, was 0.306 seconds quicker than the McLaren’s Carlos Sainz.
Vettel ended the session eighth fastest, 2.602secs slower than Leclerc.
The F1 field has convened at historic Monza five days after racing in the shadow of the death of the Formula 2 driver Anthoine Hubert on the eve of the Belgian Grand Prix.
Several drivers have revealed their feelings about Hubert’s loss and the way it has confronted them with the ever-present dangers of the sport in a more immediate way than they have become used to.
Norris, for example, has revealed that his father was sick after Hubert’s accident, and that he feels less comfortable reassuring his nervous parents that he is not going to be injured.
“I have to tell him that I will be OK, but it feels bad,” Norris said. “It is what I want to say. I am sure every driver does and then we have what happened last weekend. I am more nervous about reassuring him now.”
He admitted that Hubert’s crash was “still in my head”.
Storms overnight in northern Italy meant a wet track met the drivers at the start of practice and the treacherousness of conditions soon became clear.
Raikkonen lost control at Parabolica, spinning into the barriers and bringing out a red flag while his car was recovered.
Not long after the session resumed, Sergio Perez crashed his Racing Point on the exit of the Ascari chicane, prompting another red flag.
And there were a number of spins and moments as drivers struggled to find the limits in the slippery conditions and with ‘intermediate’ tyres which Red Bull’s Max Verstappen said over the radio were “too hard”.
There was even a third red flag after Pierre Gasly beached his Toro Rosso on the kerb after a spin at the first chicane, the Variante del Rettifilo.
By the end of the session, there had been an impressive performance from Red Bull new boy Alexander Albon, who ended up fifth fastest in his first wet session for his new team.
Verstappen ended the session seventh quickest, a second slower than Albon and behind also the Toro Rosso of Daniil Kvyat.
Mercedes’ Valtteri Bottas had a spin at the end of the session and ended up ninth fastest, 1.8secs slower than Hamilton.