Running wide at the second chicane, Hamilton dropped his wheels onto the gravel and lost a chance to improve on Bottas’ leading time.
Bottas finished a slim 0.056 seconds ahead of Hamilton with rival Ferrari again taking the third and fourth spots.
Although this time, Sebastian Vettel and Kimi Raikkonen were much more competitive, both placing within four tenths of the Mercedes.
Vettel leads Hamilton by seven points and Ferrari would like nothing more than a victory before its home fans to celebrate the automaker’s 70th anniversary.
Just after Bottas set the leading time, Hamilton had a faster pace before dropping time in the final sector.
So Hamilton will need to clean a few things up if he plans to take his fourth straight pole at Monza and break Michael Schumacher’s Formula One record with his 69th pole overall.
Hamilton led Bottas by nearly half a second in the morning.
The afternoon session was held in perfect conditions after rain fell in the morning.
With the track temperature soaring to 40 degrees Celsius (104 degrees Fahrenheit), Hamilton reported to his team via radio during a long run: “My seat’s getting really hot.”
The Red Bull cars were again fifth and sixth, with Max Verstappen leading teammate Daniel Ricciardo in a flip-flop from the morning.
There was improvement for McLaren Honda, as Stoffel Vandoorne and Fernando Alonso took the next two spots, while Esteban Ocon of Force India and Felipe Massa of Williams rounded out the top 10.
Lance Stroll spun his Williams at the Ascari chicane, bringing out the yellow flags momentarily and then Kevin Magnussen’s Haas stopped at the same spot.
“Broken suspension,” Magnussen said.
Also, smoke poured out of the back of Carlos Sainz’s Toro Rosso in an apparent engine failure.
Grid penalties are likely for both Red Bull drivers, Sainz and Alonso after engine replacements.
More rain is scheduled for qualifying on Saturday but the forecast is better for the race on Sunday.
By (AP – Italy)