Mercedes's Hamilton - last year's race winner was third quickest and 0.287 off the pace set by his fellow four-times world champion
Sebastian Vettel suffered a spin but Ferrari were still first and second in practice for their home Italian Grand Prix on Friday while Sauber's Marcus Ericsson walked away from a spectacular crash.
Vettel, hoping to make further inroads into Lewis Hamilton's 17-point Formula One championship lead this weekend, lapped the Monza circuit near Milan with a best time of one minute 21.105 seconds.
Finnish team mate Kimi Raikkonen gave the Ferrari fans - who unfurled their giant flags in the main grandstand - a further boost with the second-best time, 0.270 slower than Vettel.
Mercedes's Hamilton - last year's race winner - was third quickest and 0.287 off the pace set by his fellow four-times world champion.
He had been 11th in the morning after completing only six laps in the rain.
"We did a few laps but after that it was like having a day in the office when you don't have too much work to do -- I was even snoozing in the car at one point," said Hamilton of that wet session.
"But we did plenty of laps this afternoon in the dry and we could see that, like in Spa, we had a small gap to Ferrari on both the short and the long runs."
The main drama on a damp and overcast afternoon was provided by Ericsson.
Happy to say I'm fine after that big crash today 🙏🏻😊. Thanks for all your messages and support. Incredible how good the safety is today in @F1 . Looking forward to be back driving again tomorrow 🤙🏻💯 #ME9 #ItalianGP #F12018 pic.twitter.com/4KHKDbOnbO— Marcus Ericsson (@Ericsson_Marcus) August 31, 2018
The Swede's car speared head-on into the barriers before anyone had set a timed lap and barrel-rolled spectacularly four times along the grass verge before coming to rest as a pile of mangled wreckage.
The session was halted for 20 minutes for a track cleanup while Ericsson went to the medical centre and was given a clean bill of health.
"It was a big one. It's incredible the safety of the cars these days," said Ericsson in a video message on Twitter. "I feel fine and hopefully we can be back tomorrow and fighting."
Vettel spun off at Parabolica later but without significant damage. He kept the engine running and returned to the pits before resuming.
Heavy rain just before the morning practice saw neither of the title contenders do many laps, with Force India's Sergio Perez leading through the spray with a best effort of 1:34.000.
That marked the first time this season that one of the Mercedes, Ferrari or Red Bull drivers had not led the practice timesheets.
The Mexican, whose team were rescued from administration this month and given a new lease of life as a new mid-season entry owned by Canadian billionaire Lawrence Stroll, was eighth in the afternoon as normal service was resumed in dry conditions.
Red Bull's Daniel Ricciardo, who is using an upgraded Renault engine, was fifth and sixth but is set to take penalties that will send him towards the back of the field on Sunday.
Dutch team mate Max Verstappen was fifth and faster in the afternoon with the older specification engine.
McLaren reserve driver Lando Norris had his second Friday practice outing, after Belgium, in the morning but clocked the slowest time after running when the rain was heavy.