The 27-year-old Briton, making his 110th and final appearance for McLaren before leaving for Mercedes next year, clocked a best time of one minute and 14.131sec to outpace nearest rival and defending drivers world champion German Sebastian Vettel of Red Bull.
Vettel’s only remaining title rival, capable of stopping him becoming at 25 years the youngest triple champion in Formula One history, two-time champion Spaniard Fernando Alonso of Ferrari, was down in fifth place.
Vettel’s Red Bull team-mate Australian Mark Webber was third quickest ahead of Hamilton’s McLaren partner and Jenson Button. The top four drivers were very closely matched and were separated by just 0.086 seconds from Hamilton, who won last weekend's United States Grand Prix ahead of Vettel.
Meanwhile, Alonso and his Ferrari teammate local hero Brazilian Felipe Massa, chasing his third win on home soil, were fifth and sixth.