The Mercedes driver, who was quickest in both Friday's sessions and will be gunning for an 11th pole in 12 races, lapped the historic circuit with a best time of one minute 24.544 seconds.
Ferrari's Sebastian Vettel gave the home fans something to cheer about with the second best time, 0.264 seconds slower than Hamilton whose Mercedes team mate Nico Rosberg was third on the timesheets.
Williams drivers Valtteri Bottas and Felipe Massa, both recently confirmed for next season by the Mercedes-powered team, were fourth and fifth ahead of the Lotus of Venezuelan Pastor Maldonado and Ferrari's Kimi Raikkonen.
Daniel Ricciardo's Red Bull rolled to a stop during the session, with the team blaming a hydraulics problem. The Australian was already facing a 25 place grid penalty for an earlier engine change.
Team principal Christian Horner had said before the session that it made sense for the team to take penalties at a power circuit that they will struggle on in order to give themselves the best chance for Singapore later this month.
"Monza’s not obviously a circuit that suits us particularly. We've got the penalties as well, so you know that’s obviously a strategic thing as well - take the penalty here rather than in Singapore where we expect to be very competitive," said Ricciardo.
"Singapore, we can really fight for a podium there."
(Editing by Amlan Chakraborty)
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