Bottas had finished quickest in all three practice sessions for the Tuscan Grand Prix, and for his first time in F1, while he also edged Hamilton in Q1.
But six-time F1 champion Hamilton then took control from Q2, and come the top-10 shoot-out he produced the best lap of the weekend on his first run with a time of one minute 15.144secs, beating Bottas by 0.059s.
While Hamilton failed to improve on his second timed run, Bottas was compromised by a yellow flag in sector one caused by a spin from Renault's Esteban Ocon.
It is the 69th pole for Hamilton during his 149-race career with Mercedes, one more than Michael Schumacher managed through his 306 starts in F1.
Behind the eighth consecutive front-row lock-out for Mercedes - one shy of their own record - Red Bull's Max Verstappen starts third, with team-mate Alex Albon joining him on the second row.
On the occasion of Ferrari's 1,000th grand prix, the Scuderia at least managed to get a driver into Q3 for the first time in three races since Barcelona, with Charles Leclerc starting a superb fifth, nine places ahead of under-performing team-mate Sebastian Vettel.
For the first time in 16 races, Lando Norris failed to reach the top-10 shoot-out, with the Briton starting 11th. The McLaren driver had previously been one of only four to reach Q3 in every qualifying this year alongside Hamilton, Bottas and Verstappen.
Norris starts head of AlphaTauri's Daniil Kvyat and Alfa Romeo's Kimi Raikkonen, with Sebastian Vettel 14th after failing to make it out of Q3 for the fifth consecutive race, his worst run since 2008 when he was at Toro Rosso.
Vettel, who clearly has issues with the SF1000 as he was just over half-a-second adrift of Leclerc, has Romain Grosjean in his Haas directly behind him.
Remarkably, just six days after the glory of winning his maiden race by taking the chequered flag in the Italian Grand Prix, Pierre Gasly suffered the low of failing to make it out of Q1 for the first time in 18 races.
"He was simply too slow, he had too much understeer on the car, and he couldn't make it," was team principal Franz Tost's bleak assessment. "Very disappointed!"
Gasly missed out on a place in Q2 by just 0.053s to Vettel, who was left breathing a huge sigh of relief at the end of the session, even asking his engineer whether he made it through or not.
Alfa Romeo's Antonio Giovinazzi will line up just behind Gasly, followed by George Russell, who paid the price for catching the gravel at one stage on his final hot lap, likely costing him the 0.148s to Vettel for a place in Q2.
Russell, though, still maintained his 100% record of never being out-qualified by a team-mate in what is now 30 grands prix as Nicholas Latifi finished 0.088s adrift, while Haas' Kevin Magnussen will start last.
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