Bottas set the pace in 1 minute 26.225 seconds, with Lewis Hamilton .136 off his Mercedes teammate in second. Ferrari showed a return to form after a run of uncompetitive races, with Charles Leclerc third fastest, .456 off Bottas, and Sebastian Vettel fifth.
Ferrari reverted back to an age-old burgundy livery for its 1,000th F1 race. But there was little to celebrate as Charles Leclerc finished eighth and Sebastian Vettel 10th.
Formula 1 2020: Lewis Hamilton grabs 95th career pole in Tuscan GP qualifying as Mercedes lock front row out
Bottas had been fastest in all three practice sessions, but he was unable to maintain his superiority over Hamilton in the decisive hour.
Formula 1 2020: Valtteri Bottas hails 'fun' Mugello circuit after dominating Tuscan Grand Prix practice
Bottas clocked a best time of one minute and 16.989 seconds around the spectacular 5.245km Ferrari-owned Mugello circuit, two-tenths quicker than championship leader Lewis Hamilton with Max Verstappen a familiar third for Red Bull.
Formula 1 2020: Ferrari chief Mattia Binotto says team looking to put 'worst of days' behind at Mugello
Ferrari also finished outside the points in the previous race in Belgium and the second successive double flop dropped them to sixth in the constructors' championship.
Formula 1 2020: Pierre Gasly races to stunning victory at Italian GP as Lewis Hamilton handed penalty
Pierre Gasly finished 0.415 seconds ahead of McLaren driver Carlos Sainz and 3.358 ahead of Racing Point's Lance Stroll on a surreal-looking podium.
Formula 1 2020: Ferrari hurting after both drivers fail to qualify inside top 10 at Italian GP since 1984
After their pointless flop at the Belgian Grand Prix last Sunday, this was another embarrassment for the 'scarlet scuderia', but little surprise to their drivers.
Bottas was 0.229 seconds faster than Carlos Sainz and 0.323 quicker than Lando Norris after an impressive showing from the McLaren pair.
Formula 1 2020: 'We have to stay calm' urges Sebastian Vettel after Ferrari's dismal performance at Belgian GP
Neither Vettel nor Leclerc was able to make any impression, as Ferrari struggled and finished pointless outside the top ten.
Formula 1 2020: Charles Leclerc warns Ferrari fans to not expect ‘any miracles’ at Belgian Grand Prix
Leclerc admitted he and the team had no explanation for the team's slump in form this season — ahead of the next two races which are scheduled to take place on homeground in Italy.
Formula 1 2020: Lewis Hamilton dedicates Belgian GP pole to late Black Panther star Chadwick Boseman
Meawnhile, things are going from terrible to abysmal for Ferrari, with Charles Leclerc in 13th and Sebastian Vettel 14th.
Verstappen clocked a best lap in one minute and 43.744 seconds to outpace the Australian by 0.048 seconds, leaving championship leader Lewis Hamilton down in third for Mercedes, 0.096 adrift of the pace-setter.
Formula 1 2020: Sebastian Vettel says he has been 'happier' but quashes rumours of not completing season with Ferrari
Sebastian Vettel rejected the idea that Ferrari may ease him out of the team earlier than expected.
Formula 1 2020: Ferrari pledge full support to outbound Sebastian Vettel after string of disappointing results
Vettel, a four-time world champion, has failed to finish in the top five at any of the five opening races and came home a disappointing 12th, after a mid-race argument with the team, at last Sunday’s 70th Anniversary Grand Prix
Formula 1 2020: Sebastian Vettel’s final season at Ferrari plagued by poor performances, tense exchanges with team
Team boss Mattia Binotto says Ferrari have not lost faith in Vettel, yet it appears increasingly apparent that the German is not receiving the same level of focused support as his team-mate Charles Leclerc
Formula 1 2020: Ferrari drivers Charles Leclerc, Sebastian Vettel 'not surprised' by team's struggles
Four-time world champion Vettel, in his last season with Ferrari, qualified 12th, but gained a place thanks to a grid penalty for Renault's Esteban Ocon.
Formula 1: Ferrari driver Charles Leclerc says criticism unfair after social media charges of racism
Leclerc is one of six drivers who chose to stand and not take a knee during all four pre-race anti-racism demonstrations this season.
Formula 1 2020, British GP: From Hamilton's dramatic win to Leclerc’s unexpected podium, talking points form race
Lewis Hamilton secured his 87th career victory At British GP despite a tyre failure on last lap but Valtteri Bottas and Carlos Sainz tumbled out of the points during closing laps due to similar issues.
Formula 1 2020: Lewis Hamilton grabs pole position at British GP qualifying ahead of teammate Valtteri Bottas
Hamilton needs five more wins to equal Michael Schumacher’s Formula One record of 91 GP wins. The defending champion is also odds-on to equal the F1 great's record of seven world titles.
Formula 1 2020: Only Valtteri Bottas can stop Lewis Hamilton from winning the driver's championship, say Ferrari drivers Sebastian Vettel, Charles Leclerc
Hamilton dominated Sunday’s Hungarian Grand Prix from pole position, with a bonus point for fastest lap, to take a five point lead over Bottas, the winner of the Austrian season-opener.