Red Bull's championship leader Sebastian Vettel was fourth fastest.
Hamilton, who will be chasing his fifth pole position in a row on Saturday, roared around Monza's classic 'Pista Magica' with a best time of one minute 25.565 seconds on a sunny morning in the former royal park.
The Briton, who was booed by some of the passionate Ferrari 'tifosi' when he won for McLaren last year, had said on Thursday that he hoped they would be booing him again if it meant a return to the top step of the podium on Sunday.
The 2008 world champion certainly has a good chance, as one of only three current drivers to have won the final round of the European season and with Mercedes looking increasingly competitive.
Vettel and Alonso, the top two in the championship after 11 of 19 races, are the other two past winners with the German triple champion 46 points clear of the Ferrari driver.
Alonso might have gone quicker than Hamilton had he not run wide, kicking up a cloud of dust, at the exit to the Parabolica corner on a fast lap with half an hour to go.
Raikkonen suffered his first retirement of the season, ending a 27-race scoring run, at the previous race in Belgium and has fallen back to fourth in the championship behind Hamilton.
A banner in the start/finish grandstand, written in large red letters and positioned next to a Ferrari flag, declared 'Kimi in pole' in what looked like a throwback to 2007 when the Finn finished third at Monza for the Italian team.
Raikkonen has a longer wheelbase car for the race, the fastest on the calendar with speeds of up to 340kph, but has played down his chances.
"It will be very difficult," he told reporters. "The low downforce circuits are probably not the strongest for us. Last year was difficult, and last year at Spa was quite tricky, and it wasn't easy this year either."
McLaren were sixth and seventh fastest with Mexican Sergio Perez and Britain's Jenson Button, who had a DRS problem with the rear wing, while Australian Mark Webber was eighth for Red Bull in what will be his final F1 appearance in Europe.
His 2014 replacement, compatriot Daniel Ricciardo, was 13th.
Ferrari's Felipe Massa, whose race seat is once again in the spotlight with endless speculation about who might replace the Brazilian next year, was a disappointing 14th.
Britain's James Calado made his debut at a grand prix weekend, the newly-appointed Force India third driver taking over Adrian Sutil's car for the morning session before the German returns after lunch.
He did 24 laps and was 17th fastest.
Caterham and Marussia also ran their reserve drivers, Finland's Heikki Kovalainen and Venezuelan Rodolfo Gonzalez.
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