McLaren lock front row in Italy
Hamilton clocked 1:24.010 minutes in the dying minutes of Q3 displacing Ferrari's Felipe Massa.
Teammate Jenson Button came in second, moving up the table with 1:24.133 as he became the last car to cross the line under the chequered flag.
Driver's championship leader Fernando Alonso of Ferrari was unable to match his performances from earlier in the session and finishing 10th, more than one and a half seconds behind Hamilton (1:25.678).
Teammate Felipe Massa will line-up third overall after out-qualifying the Spaniard, who appeared to make a mistake at the first chicane on his final flying lap.
Sahara Force India's Paul di Resta briefly held second spot before being deposed by Massa and then Button, but the Brit will take a five-place grid penalty which drops him to an eventual ninth, sharing row five with Alonso.
Michael Schumacher finishing fifth will move up to take di Resta's fourth spot, with Sebastian Vettel, who only just made it into the final phase of the session, assumed the inside of row three for Red Bull.
The German will be joined by countryman Nico Rosberg of Mercedes while Lotus' Kimi Raikkonen and Sauber's Kamui Kobayashi fill row four.
Earlier Red Bull driver Mark Webber went out in Q2 as he failed to qualify for the final session while Force India's Nico Hulkenberg was eliminated in Q1 after a gear box problem.
India's Narain Karthikeyan beat HRT teammate Pedro de la Rosa and will start 22nd setting a time of 1:27.441.