The Mercedes driver was more than a second quicker than Red Bull's Max Verstappen, the second fastest in a much-delayed session that ended more than three and a half hours after it started.
Verstappen and Australian team mate Daniel Ricciardo both have grid penalties, which means Canadian teenage rookie Lance Stroll will move up from fourth to start on the front row for Williams.
Vettel will also move up to sixth position as a result of those penalties.
Hamilton, who is seven points behind championship leader Vettel and can take the overall lead on Sunday, equalled Michael Schumacher's all-time record of 68 poles last weekend in Belgium.
It was the fourth year in a row that the Briton has taken pole at Monza, the fastest circuit on the calendar.
(Reporting by Alan Baldwin; Editing by Greg Mahlich)
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