The Mercedes driver clocked the fastest lap with a time of one minute and 23.383 seconds to finish three tenths clear of Ferrari's Kimi Raikkonen who will begin Sunday's race at the front of a Formula 1 grid for the first time since 2013.
Raikkonen took advantage of the misfortune that befell Hamilton's teammate and primary title rival, Nico Rosberg, who was forced to change engines before the session began. The German could only finish fourth as a result, his worst qualifying performance of the year.
Sebastian Vettel, also of Italian manufacturer Ferrari, pipped Rosberg into third position to the delight of the home crowd.
Rosberg trailed Hamilton by 28 points in the race for Driver's Championship coming into the weekend. But the Briton appeared more focused on continuing Mercedes' dominance of recent years than on his ever spiky duel with Rosberg when speaking to the press Saturday.
"I hope Nico can pull through tomorrow and we can finish ahead of the two red (Ferrari) cars," Hamilton said in comments carried by the AFP news agency. "But they are very close here and it is going to be a tough race."
Ferrari's strong showing was especially encouraging for the partisan Italian crowd and for 2007 F1 champion Raikkonen.
"We expected a strong weekend, knew this place was not our strongest and the car turned out to be pretty good," he said.
The Finn added: "It is nice to be here. It's a home race for us and this was our best qualifying performance this year as a team. Now we will try and have another go to get a good result tomorrow."
Getting close to Lewis
For Vettel, just getting close to Hamilton in the Mercedes car which has been by far the fastest in F1 in recent years was enough to give him hope of something special on Sunday.
"We are close to Lewis and that will give us confidence," Vettel said. "I hope we both finish ahead of him, that would be a dream come true.
"But the Mercedes has serious pace which we have found out many times and we will have to fight and do all we can."
Felipe Massa was fifth fastest ahead of his Williams team-mate Valtteri Bottas while Sergio Perez of Force India and Frenchman Romain Grosjean of Lotus followed in seventh and eight position respectively.
Nico Hulkenberg was ninth for Force India ahead of Marcus Ericsson of Sauber.