Leclerc had looked like a real contender for pole position after setting the pace by just over 0.1secs in the second knockout session.
Hamilton made an uncharacteristic mistake in his first shot at pole, temporarily losing control of his vehicle through the left-handed Brooklands.
But Ferrari's deficit appeared a lot more sizeable in longer runs, and Leclerc marked this out as the overriding concern during what he felt was "not a great day".
Mercedes failed to win for the first time this season last time out in Austria and you can be sure the world champions will be eager to get back onto the top step of the podium.
The 21-year-old Mongasque will start the race on the soft tyre, while the Mercedes and Red Bulls will use the medium.
With the trio of big events, the clashes are proving even more problematic than last Sunday, when three soccer finals were played on three continents in different time slots: the Women's World Cup in France, the Copa America in Brazil and the CONCACAF Gold Cup in the United States.
Here is how to watch all the action from race at Silverstone LIVE and for FREE. George Russell and Robert Kubica were in 19th and 20th for Williams. "It reminds me why you do it, for these kinds of feelings".
"It feels very good", Bottas said after qualifying.
"The first lap was good but not flawless and I should have improved on the second run but I couldn't get the lap together". "These cars all have sweet spots", said Hamilton, victor of six of this season's nine races so far.
"It was not easy today and I think everyone was making mistakes here and there, but the lap was good enough", said the Finn. "Without people like this to fill it up, and bring energy it would be nothing, so that is why we have got the best fans in England". "We had better years [in] recent years than the years before, so that's good". If we manage to gain some positions at the start, it's a track where it's quite hard to overtake so then we have some chances to keep them.
"Normally we can [tune it out], but somehow, today, we couldn't".
"But I hope in future that they put this on - this is such a special weekend that it needs all the focus of the whole country".
And the new Mercedes entry will be able to draw on the expertise of their all-conquering F1 counterparts with James confirming there will be close ties between the two teams. We tried a couple of things and maybe some of them will go back.