The Dutchman punched in a 1m30.688s to stand atop the timing boards, having been bumped off the top following his opening run on soft tyres as the rest of the front-running pack waited until later in the session to clock their first times on softs.
Verstappen had originally gone quickest with a 1m31.377s on his first timed run, going early on soft tyres as the majority of the field used the early part of the session to explore Pirelli's prototype tyre compound.
But his lap was knocked off the top by Lando Norris, who switched to a set of the red-walled tyre and set a 1m31.152s to underline McLaren's pace on the technical and flowing Suzuka course.
Leclerc then moved above the Briton with a 1m31.008s, as Ferrari looked to retain its advantage over the other teams chasing second in the constructors' championship from Singapore. Last weekend's winner Carlos Sainz continued to demonstrate Ferrari's strong package by slotting into third, behind Norris.
After Red Bull had been widely tipped for a resurgence over the Japanese GP weekend, Verstappen proved that hypothesis further having logged the first time below the 1m31s bracket - going just over three-tenths ahead of Leclerc's earlier headliner.
As this preceded the customary long-run simulations as the teams sought to assess tyre performance and degradation in preparation for Sunday's race, Verstappen's time remained untouched in the final 20 minutes and the Dutch driver remained clear of Leclerc for the remainder of the session.
Source: Autosport