Leclerc, who trails leader Max Verstappen by nine points in the championship standings, bounced back from his Monaco misery a fortnight ago, to blow away his rivals.
The Monegasque saw off Sergio Perez, who took advantage of Leclerc’s flat-footed Ferrari team in Monte Carlo to claim his third career win, by 0.282 seconds.
World champion Verstappen lines up in third place, one spot ahead of Ferrari’s Carlos Sainz. George Russell out-qualified teammate Hamilton for the fifth time in eight rounds this season.
Russell will start fifth on Sunday, two places ahead of Hamilton, who could drop further down the field if he is penalised for his qualifying misdemeanour.
Hamilton, who finished an eye-watering 1.6 secs behind Leclerc and two tenths adrift of Russell, appeared to delay fellow countryman Lando Norris in the final minutes of Q2.
While Hamilton progressed to the top-10 shoot-out, Norris was eliminated and finished 11th.
Norris’ race engineer Will Joseph said to his driver of Hamilton: “He is the lead car, he will get in trouble.”
After claiming his sixth pole of the season and fourth in succession, Leclerc said: “All poles feel good but this one I did not expect because I thought the Red Bulls were stronger.
“But the last lap came together and I am extremely happy. I am really excited for tomorrow.”
Hamilton, who heads into Sunday’s race 75 points behind championship leader Verstappen, has endured a trying weekend here and was warned by his team not to drive slowly on his out-lap.
He responded by saying: “I don’t know what you expect from me, man, sometimes.”
Hamilton has been summoned to the stewards on Saturday evening and faces a possible grid drop if he is found guilty of a rules breach.
Hamilton’s Mercedes team continue to struggle with porpoising here.
“The car is bottoming a dangerous amount,” said Hamilton as he hit speeds approaching 220mph.
Q1 was red-flagged with just two-and-a-half minutes remaining after Lance Stroll crashed out.
Only moments after thudding the barrier, before reversing out of trouble, the Canadian driver hit the wall for a second time.
Stroll carried too much speed through the second bend, losing control of his Aston Martin and collecting the tyre barrier.
Stroll was forced to park his wounded machine as race director Niels Wittich deployed the red flag.
A 10-minute delay ensued for track repairs before a frantic dash to avoid falling at the first hurdle. Haas’ Kevin Magnussen and Alex Albon and Nicholas Latifi of Williams were eliminated.
The struggling Mick Schumacher also failed to improve and will line up in 20th and last position for the race.