At the Suzuka circuit rated by many drivers to be the best in Formula One given its figure-of-eight configuration, Hamilton was comfortably quickest by a third of a second from team-mate Nico Rosberg.
The Briton, only mathematically in this season's title race as he is 111 points adrift of Sebastian Vettel with a maximum 125 remaining, set a time of one minute 34.157secs.
With Rosberg for company at the head of the timesheet, the duo kept Vettel at bay, with the 26-year-old German 0.611secs down.
Vettel could conceivably win his fourth consecutive F1 world title on Sunday should he chalk up a fifth successive win this year and rival Fernando Alonso finish ninth or worse.
The track is also one Vettel has made his home as he has been on pole for the last four years, winning three times.
Behind Vettel was Red Bull-team-mate Mark Webber, with the Australian sporting a chassis last used in Hungary given the repairs required to his car following the fire sustained in Korea on Sunday.
Webber finished just 19 thousandths of a second behind Vettel, but considerably ahead of the Ferrari duo up next in Felipe Massa and Alonso, both of whom were just under a second down.
Given the two-by-two nature of the top order, the Lotus' were up next, with Romain Grosjean 1.022secs behind Hamilton and two tenths ahead of team-mate Kimi Raikkonen.
The McLarens were unable to follow suit, with Sergio Perez and Jenson Button ninth and 11th, separated by Toro Rosso's Daniel Ricciardo in 10th.
Button finished 1.711secs down, with Force India's Paul Di Resta 17th and 2.242secs adrift at the start of a weekend when he needs a good result after a run of six races without scoring a point.
Renowned for being an unforgiving track, with no quarter given should a driver make a mistake, Suzuka witnessed three incidents during the opening 90 minutes.
Two appeared to be driver error, whilst the other appeared to be a concern as the left-rear wheel of Pastor Maldonado's Williams inexplicably detached itself from the car.
Approaching Spoon Curve, Maldonado ran wide, but as he attempted to make his way back on track, the Venezuelan was forced into a spin as the wheel worked loose, it then bouncing into a gravel trap where it was recovered by marshals.
With just three wheels, Maldonado at least managed to park up his car in a safe place off track.
That was followed moments later by Caterham's Giedo van der Garde locking at the second Degner corner, resulting in the Dutchman ploughing straight on into a tyre barrier.
On this occasion the marshals were forced to employ a crane to lift the car out of the trap, transporting it to a spot where Jules Bianchi's battered Marussia was waiting to be taken back to the garage.
Earlier in the session Bianchi also hurtled into the tyre wall at the second Degner, severely damaging the front-left of his car.
It is understood in attempting to turn into the corner, Bianchi trapped his arm between his seat and the chassis, leading to the Frenchman later sitting in his team's hospitality unit wearing an ice pack to his left elbow.
Maldonado eventually finished 15th on the timesheet, with Bianchi and Van der Garde down in 20th and 21st as Marussia's Max Chilton again brought up the rear, finishing 4.606secs adrift, the Briton surviving his own spin in the final minute.