The 28-year-old German clocked a best lap time of one minute and 24.781 seconds at the spectacular Interlagos circuit early in the 90 minutes' action and, as the rain intensified, it proved to be untouchable.
Briton Hamilton, the 2008 world champion, was second in 1:25.230 ahead of four-time world champion German Sebastian Vettel of Red Bull and the 2009 champion Jenson Button of McLaren.
Two-time champion Fernando Alonso of Ferrari was fifth-quickest ahead of his friend, retirement-bound Australian Mark Webber, who competes in his final race with Red Bull this weekend.
Mexican Sergio Perez, in his last weekend with McLaren, was seventh ahead of impressive 19-year-old Russian rookie Daniil Kvyat, running for Toro Rosso ahead of his move to replace Red Bull-bound Australian Daniel Ricciardo next season.
Mumbai Roundup: 9 incidents that took place this week
Photos: Ajay Devgn, Parineeti, Tabu at 'Golmaal Again' trailer launch
Photos: Dipika Pallikal Karthik oozes oomph in bikinis and sarees
Photos: Kareena Kapoor Khan's grand birthday bash
Photos: 'Dangal' girls Sanya Malhotra, Fatima Sana Shaikh's dinner outing