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 results, 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 Autosport 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."
Source: Autosport