In a pulsating session, Hamilton had crossed the line at Silverstone with a provisional pole lap, only to be beaten by Bottas moments later with a lap of one minute 25.154s to claim the 13th pole position of his Formula 1 career.
Following all the furore over Racing Point this week and the brake duct protest and subsequent intentions to appeal by four of its rivals over the leniency of the penalty,
Nico Hülkenberg claimed a stunning third position.
Serving as substitute for Sergio Perez, who again tested positive for Covid-19 this week, it proved to be Hülkenberg's best qualifying since Austria 2016.
The position now offers the German the chance to rid himself of an unwanted F1 record as he has yet to finish on the podium from his previous 177 starts.
What unfolded with Bottas and Hamilton was hardly a surprise as the duo had finished one-two in each of the three practice sessions for this weekend, while they also locked out the front row for last Sunday's British Grand Prix. This was the 67th in the team's history.
The top three will all start on the medium-compound Pirellis, so at least Red Bull's Max Verstappen offers something different as he will be on the hard tyre in starting fourth.
Daniel Ricciardo, like Hülkenberg, produced a stunning performance to deliver up fifth for Renault, followed by the second Racing Point of Lance Stroll, who finished a third of a second behind Hülkenberg.
Esteban Ocon qualified 11th but is under investigation by the stewards for impeding Williams' George Russell in Q1 through Aintree.
The Frenchman faces a near-certain three-place grid drop for an incident described by the Briton over the team radio as "massively dangerous".
If punished, that will elevate Sebastian Vettel by one position as the four-time F1 champion again failed to make it out of Q2, finishing 0.3s down on Leclerc as he failed to hook up his SF1000 around the Northamptonshire circuit.
Vettel even attempted his last flying lap on the soft tyres to get him into Q3 but still fell short.
For the first time this year, McLaren failed to get both cars in Q3 as Carlos Sainz could only qualify 13th, out-qualified for the fourth time in five races by Norris, with Haas' Romain Grosjean 14th, although a penalty for Ocon will push them up a grid slot.
For the fourth successive race, Russell again delivered Williams a Q2 spot as he will line up 15th.
Daniil Kvyat would have made it into Q2 only for his last flying lap to be deleted after he ran wide at Stowe, so exceeding the track limits, and he will start 16th.
That appeared to stem from the fact the Russian had earlier run wide over the Chapel kerb which led to him declaring over the team radio that "something on the floor broke".
Magnussen, who was bottom of the timesheet in FP2 and FP3, at least managed to avoid that ignominy in qualifying and will line up 17th, albeit the Dane finished seven-tenths of a second behind team-mate Grosjean.
Williams' Nicholas Latiifi starts 18th, beating both Alfa Romeos as the team maintained its record of failing to get a car out of Q1 this season, with Antonio Giovinazzi ahead of 2007 world champion Kimi Raikkonen.
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