While Bottas stayed in the garage in second practice, Hamilton felt it important to give the spectators something to watch.
For tomorrow's race, the following drivers have grid penalties, Bottas (5 places), Raikkonen (5 places) and Alonso (35 places).
Raikkonen finished in sixth but has a five-pace grid penalty for replacing his gearbox after the damage he sustained going off at the second Degner during final practice on Saturday morning.
"Also the Red Bull is coming back up, so I just hope we have the strength to be able to fight back", added Hamilton.
Vettel is still seen as somewhat of a favourite on Sunday and his opening drive in first practice highlighted that fact.
Lewis clocked in at one minute, 27.319 seconds.
Hamilton knows only too well of the threat Ferrari poses due to its superior speed on the Suzuka track, despite what has been a hugely humbling section of the F1 calendar where Vettel was set to open up a decision lead in the race for Dubai's finale. Japan has now staged over 30 races and almost half the stagings have seen the world champion crowned, due to when it takes place.
Vettel's best time of 1m29.166s was set shortly after a red-flag period that was caused when Toro Rosso driver Sainz suffered a violent crash around 50 minutes into the session. With only 78s left in the session, there was barely enough time for second runs.
Hamilton offered a sign of things to come in Q3 by breaking the previous Suzuka track record held by Michael Schumacher in the second stage of qualifying, going nearly a second faster than the previous benchmark.
Various grid penalties will mix up the provisional starting order.
Hamilton started Q3, followed by the rest of the field except for Alonso. The other two compounds available were the medium and super soft.
Hamilton, although, is leading the championship with two hundred eighty-one points, the British had to be satisfied with the second position in Malaysian GP. The top five after the first runs were Hamilton 1m27.345s, Vettel 1m27.797s, Bottas 1m27.986s, Ricciardo 1m28.444s and Verstappen with a 1m28.985s.