The Dutchman, who is hoping to win a record-breaking tenth consecutive grand prix this weekend, set a lap time of 1:22.657 seconds at the Monza circuit.
He was only 0.046s clear of birthday boy Sainz in second with Red Bull team-mate Sergio Perez lining up in third.
Even though Verstappen still managed to come out on top, the teams looking to overhaul Red Bull can take comfort from the fact that the margin was very small.
That is particularly the case with Ferrari as they seek to impress the loyal Tifosi who were already loudly backing them from the grandstands.
Sainz, celebrating his 29th birthday, set a lap time less than a tenth of a second shy of Verstappen's, indicating there could be a real battle this weekend.
Perez was followed by Leclerc who finished fourth despite spending the first part of the session up on the jacks.
Sky F1 pit-lane reporter Ted Kravitz said this was simply for the team to test out new 'aero parts' and he ended the session three-tenths shy of Verstappen's time.
Mercedes duo in the mix
Many eyes this weekend will be on the progress made by Hamilton and Russell following the news they signed new two-year deals to the end of the 2025 season.
Like Red Bull and Ferrari, their top 10 times were set on the hard tyre with Russell fifth while Hamilton was slightly behind in eighth.
It was a relatively straightforward session for the Mercedes team, though Hamilton did draw the ire of AlphaTauri's Yuki Tsunoda who complained on team radio that Hamilton 'does not know how to get out of the way'.
Williams have been getting better throughout 2023 and once again they had a car in the top 10 with Alex Albon finishing 10th, just shy of a second adrift of Verstappen at the top.
The British-Thai driver, racing in Monza a year after appendicitis forced him to sit out the Italian Grand Prix, had a frightening moment at the Ascari chicane when he lost control of his car sending it onto the grass.
However, he was able to carry on virtually unscathed and he will be targeting a Q3 position on Saturday, as will team-mate Logan Sargeant who finished 12th.
Despite sporting a striking new livery bearing the Italian flag, it was not a happy session for Alfa Romeo with problems affecting both Valtteri Bottas and Zhou Guanyu.
Both cars were suffering from software issues early in the session, linked to problems with the anti-stall system, and that cost them valuable track time.
When they did get on, the pair almost in unison complained to the team the car was 'undrivable' and that was reflected in the times.
Bottas finished the session 15th after some improvements while Zhou was dead last in P20.