With teams aware of the prospect of an FP2 wash-out, the FP1 times served to provide a greater indication than usual as to the relative pecking order for the weekend.
The German, who trails Hamilton by 34 points in the standings with five races to go, was 0.324 seconds down on Bottas' mark despite lapping on the stickier super-soft tyre compared to the less grippy softs Bottas and Hamilton set their fastest laps on.
He said: "It's been an interesting day, the auto is feeling much better than it was in Malaysia".
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.
However, Ferrari have said the gearbox is in fact "still available" to use in Japan.More news: Las Vegas massacre: Gun lobby's surprise response
"I don't know which sort of pace they will have", he said.
"It was a decent morning", Vettel said.
"For us normally we are a bit stronger in the race compared to qualifying, so we get together and see what we can do at the start and during the race". The world champion responded with a faster time of 1m29.047s. He was unable to minimise the cost, however, with both Red Bull's beating the Finn to fourth and fifth at a circuit Ferrari should expect to be the next quickest behind Mercedes. "I'm not here to finish second in every race to do the job - I want to win convincingly".
Practicality is one thing, out giving the fans is something else, and Hamilton was one of only five drivers who deemed it worthwhile giving them something to cheer as FP2 was rained out.
The Spaniard told F1.com that even the smallest of mistakes can be punished by the challenging Suzuka track.
But team boss Toto Wolff was optimistic of a better weekend in Japan, telling Sky F1: "Malaysia was a combination of factors that didn't particularly suit us - the heat being the most important one". He was coming out of the hairpin at turn 11 and got out onto the kerbs, spinning the rear and smacking him into the wall at high speed, nearly flipping the auto.
Title hopes aside, the Japanese race is made all-the-more exciting thanks to the Suzuka Circuit, originally a test track for Honda, it is a high-speed circuit famous for its figure-of-eight layout formed by a total of eighteen corners.