Hamilton's lap of 1:12.458 edged out team mate Jenson Button by less than a tenth of a second.
Mark Webber lines up in third place, with Sebastian Vettel only fourth.
Felipe Massa and Pastor Maldonado share the third row, ahead of Nico Hulkenberg and Fernando Alonso.
Kimi Raikkonen and Nico Rosberg rounded out the top ten.
The session started in damp conditions, which meant that the early runners struggled for grip, particularly in Sector 3.
Romain Grosjean's eagerness to pass the HRT of Pedro de La Rosa saw the two make contact at the final, flat out corner, with the Frenchman losing his front wing and ending up in eighteenth place.
Home racer Bruno Senna finished in twelfth place, while Michael Schumacher managed fourteenth in his final qualifying session.
Paul di Resta narrowly failed to make it through to Q3, as did the Sauber drivers of Sergio Perez and Kamui Kobayashi.
Both Toro Rosso drivers made it to Q2 but were sixteenth and seventeenth, while at the back, Vitaly Petrov edged out Heikki Kovalainen by 0.013s to claim nineteenth place.
Timo Glock, Charles Pic, Narain Karthikeyan and the damaged HRT of Pedro de La Rosa complete the grid.