Following his triumph last year around Monza, Hamilton stepped onto the top step of the podium and was roundly jeered by the 'tifosi', the Italian term used to describe Ferrari's passionate fans.
It has become a tradition that any driver not wearing Ferrari red is booed should they make it into the top three.
Hamilton revealed on Thursday he would pay to be booed again as that would mean he had taken the chequered flag for a second successive year around one of the most revered of venues.
Following the opening 90-minute practice session, Hamilton finished top in his Mercedes with a lap of one minute 25.565secs, set on the hard, slightly slower Pirelli tyre, as opposed to the medium due to be used in the second run.
Nevertheless, after a trio of practice sessions for the Belgian Grand Prix a fortnight ago where Mercedes struggled with their package, this was a return to form for the German manufacturing giant.
With the car boasting a Monza-specific package due to the high speeds and low downforce of the circuit, Hamilton finished 0.035secs ahead of Ferrari's Fernando Alonso.
With Hamilton third and Alonso second in the drivers' standings, 58 and 46 points adrift respectively, both men know they need a strong result this weekend to eat into Sebastian Vettel's lead.
Vettel was fourth quickest in his Red Bull, 0.188secs down, and just five hundredths of a second behind Nico Rosberg in his Mercedes as the latter manufacturer suggested they are poised to enjoy a positive weekend.
Lotus' Kimi Raikkonen, who has fallen 63 points behind Vettel after suffering his first retirement for 39 races at Spa, was fifth in a long-wheelbase car as the team try something different to remain in the title hunt.
The concept was only being used by Raikkonen, with team-mate Romain Grosjean down in 12th position and a further four tenths of a second back.
The McLarens of Sergio Perez and Jenson Button, neither of whom has finished on the podium this season in what has been a miserable year for the team celebrating their 50th anniversary this weekend, were an intriguing sixth and seventh on the timesheet, just under half a second down.
Red Bull's Mark Webber, the Williams of Pastor Maldonado and Jean-Eric Vergne in his Toro Rosso completed the top 10.
The speed of the circuit is such that the top 14 were all covered by a second, although the two Force Indias of Paul Di Resta and James Calado were outside that time.
Di Resta was 15th quickest, 1.029secs back, with Calado on his F1 debut as the team's reserve, a highly commendable further four tenths adrift.
Another reserve in Marussia's Rodolfo Gonzalez brought up the rear, almost four seconds down and 1.6secs behind team-mate Max Chilton.