The championship leader and defending three-time champion clocked a best lap time of one minute and 21.135 seconds to outpace the German by nearly half a second.
The 'silver arrows' dominated the session to finish comfortably ahead of the Ferraris of Sebastian Vettel and Kimi Raikkonen.
"I was right in the sweet spot today and I was able to get an exceptional lap time out of it," said Hamilton. "What this team has achieved in phenomenal."
It was also the 56th pole of Hamilton's career.
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Senna was the last man to achieve a hat-trick of Italy poles.
Hamilton and Rosberg's front row lockout was Mercedes' 41st and enabled them to equal the record of dominance set by Red Bull pairing Vettel and Mark Webber in their heyday.
Hamilton will be bidding on Sunday to register a hat-trick of Italian wins with his 50th career victory to enlarge his nine points lead in the title race ahead of Rosberg.
Valtteri Bottas was fifth for Williams ahead of Australian Daniel Ricciardo and his Red Bull team-mate, Dutch teenager Max Verstappen.
Sergio Perez was eighth ahead of his Force India team-mate Nico Hulkenberg with Esteban Gutierrez taking 10th for Haas.
"I feel proud and honoured to be mentioned amongst such greats as Senna and Fangio. Never in a million years did I expect my name to be mentioned in the same sentence and I am very proud of that."
Vettel admitted: "The gap is quite big... The guys ahead of us are in a world of their own."
The session began in near-perfect conditions, with late-summer sunshine bathing the old royal park north of Milan.