Hamilton refused to be drawn on his future in the build-up to the race weekend, but turned in one of his best performances of the campaign - dominating the practice sessions, taking top spot in qualifying then wrapping up the victory.
It would have been better still for McLaren had Jenson Button not suffered a mechanical fault when running comfortably in second place on lap 35.
Second went instead to Sergio Perez, who drove superbly from 12th in the Sauber to make a one-stop strategy work, scything through the field in the latter part of the race.
Fernando Alonso made way for the Mexican and settled for third, but given his start place of 10th, and the misfortunes of his Red Bull rivals, it was a day to savour for the Spaniard.
Sebastian Vettel and Mark Webber both had to retire with a handful of laps remaining on a wretched day for Red Bull, meaning Alonso now leads the world championship by 37 points from Hamilton.
Kimi Raikkonen held on to fifth place from the charging Mercedes pair, while Paul di Resta, Kamui Kobayashi and Bruno Senna rounded out the top 10.
On a bright summery day in Italy, there were high hopes from the tifosi that despite starting 10th, Alonso could recover and put in a drive to delight the home crowds.
Alonso and team-mate Felipe Massa gave the team the best possible start, with the Brazilian leapfrogging Button into second, and Alonso gaining four places in quick time.
Button, opting for a one-stop strategy, won that place back on lap 19, while Hamilton eased into a position of safety at the front. There was no great shake-up behind the leaders, despite the majority of drivers making their pit stops over a fairly wide spread of laps.
Vettel and Alonso made their stops on the same lap, however, coming out just a whisker apart, and the Spaniard was soon on the world champion's rear wing. A passing attempt on lap 26 ended with Alonso on the grass; the Ferrari man believed he had been forced off, and stewards agreed, enforcing a drive-through penalty. Vettel lost further grid position, finding himself stuck behind his team-mate; meanwhile Alonso closed on his, Massa, for an easy pass.
But the real story was Perez - having stayed out longer than his rivals and run briefly in first, he had the fresher rubber, and carved his way from eighth into second.
Mercedes, seemingly running off the pace all day, also made hay in the latter stages. Their two-stop strategies saw Michael Schumacher leap back up to sixth, with Nico Rosberg just behind him.
Ferrari fans cheered Alonso's third place as if it was a victory - and with seven races remaining, and the championship lead stretching, it will have felt like one.