Verstappen looked to have the measure of the field throughout qualifying, bouncing back from a Q2 elimination in Singapore to take pole by around six tenths from McLaren's Oscar Piastri and Lando Norris.
But while the McLarens were delighted by their top three result, Ferrari was more puzzled by the chasm to Verstappen after Carlos Sainz won last week's Singapore Grand Prix from pole.
Leclerc was fourth almost seven tenths in arrears, with Sainz nearly a second down in sixth behind the second Red Bull of Sergio Perez.
Afterwards, Leclerc's eyes lit up when asked by Motorsport.com how surprised he was by the gap to Verstappen's spectacular pole lap, which was hailed by the Dutchman's team boss Christian Horner as "mind-blowing".
"It's crazy, they've been really on it straight from FP1," Leclerc replied.
"We understood that there was quite a bit of work to do, especially in sector one for some reason, because there we are losing most of the time we are losing around the lap."
Leclerc's deficit to Verstappen spoiled what he felt had actually been a nearly optimal Q3 lap.
"Happy is a big word but I'm happy with my own performance, because I think it was a really, really good lap and I don't think there was much left in that lap.
"That was great, but I mean, it's only P4, so that's a bit of a shame. [Suzuka] feels amazing but it's a bit disappointing when you finish such a great lap and then you're P4, and seven tenths off too."
Perez was also left frustrated after conceding seven tenths to Verstappen's "tremendous" lap after having struggled with the balance of his Red Bull all weekend.
He felt having to sacrifice an extra set of fresh softs to get comfortably through Q2 then came back to bite him as he lost out to Leclerc and both McLarens in Q3.
"Max has been very strong," he replied when asked about his reaction to Verstappen's 1.28.8 pole lap.
"I mean, when we see the difference that he is making, he's definitely had a tremendous lap. Well done to him.
"Definitely the front row was in the car today because [using] that second set in Q2 was not ideal. And that put us on the back foot to the McLaren mainly by just having one set of new tyres, so that was not ideal.
"But anyway, let's look forward to tomorrow. I believe that on race pace we are strong, we have good tyre degradation. That's going to be quite critical tomorrow.
"Hopefully we can finish with a one-two tomorrow and that will be a great way to seal the constructors' championship."
