Palmer and Sainz, however, both have 20-place grid penalties for power unit changes.
Hamilton and Bottas both used the Soft and SuperSoft compound tyre in first practice. Hamilton went fastest, albeit lapping almost 20 seconds slower than Vettel's morning benchmark. He will start alongside Sebastian Vettel tomorrow thanks to a Bottas gearbox penalty, which is what people want to see.
With the first runs done, Magnussen was 15th and on the bubble with Grosjean 16th and Vandoorne 14th.
After a tough few weeks, Vettel says Ferrari are confident of a good race in Japan.
The top seven stayed in the pits for the remaining minutes while the others went back out.
There was plenty of drama on Saturday, as Romain Grosjean lost control of his Haas in Q1 and suffered a spectacular crash. His first sector - the most demanding and rewarding of the lap - especially through the esses, was absolutely mighty and he used every inch of the track and the enhanced engine mode Mercedes is able to employ over a single lap.
In a display of utterly scintillating driving, Hamilton whittled away at the track record to secure himself provisional pole - and Bottas snuck in behind him to take P2, although again with grid penalties that won't be a lock-out for Mercedes.
Vettel focused on race simulations early in the session, before turning his attention to the super-softs and low fuel.
When practice resumed after a 10-minute halt to remove debris from Bottas's vehicle, Raikkonen soon followed suit, shunting his auto into a wall and bringing another halt to proceedings.
Were Verstappen and Ricciardo to become the filling in a red and silver sandwich, finishing behind the two Ferraris but ahead of the Mercedes pair, then that would change everything.
Could anybody beat Hamilton during the 12 minutes of Q3? All three sessions were filled with drivers locking up and running wide as they continued to explore the limits. Hamilton's best laps were the quickest ever completed around the Suzuka circuit and onboards suggested there were areas he could have improved further.
While Mercedes is yet to fully get to the bottom of its Malaysian malaise, Hamilton was feeling encouraged by his limited time in the vehicle on Friday at Suzuka. He ended up with a best of 1:27.319 to win pole.