The German was 0.211 seconds quicker than Hamilton, who leads Vettel by 34 points with five races remaining.
Hamilton said Mercedes had "definitely still question marks" about the car's performance but added: "I saw some stories that we had been thrown off the ball or are on the back foot".
"I'm glad that we had the dry session for FP1", he said. "The auto felt a lot different to what we had in Malaysia, which is a good thing". "But I think the Ferraris did bring quite a big upgrade in the last race so it's going to be interesting to see that probably being unleashed and also the Red Bull is coming back up".
While Bottas stayed in the garage in second practice, Hamilton felt it important to give the spectators something to watch. I was like, 'Let's just go, ' they were like, 'No, no we wait.' I was like, 'Look I want to go out, ' so they let me out. Each race is really just about trying to understand more about the vehicle because there is constantly something new coming in the mix that can catch us off guard.
But, despite the limited running, Hamilton is in an optimistic mood.
The Dutchman ran wide through the gravel at the Spoon double left-hander midway through the session and then bounced over the kerb on the exit of the tricky Degner Two corner.
"The vehicle did feel better than it did in Malaysia, but we still need to work on things to make the auto quicker", he said.
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Conditions were so bad that the start of FP2 was delayed indefinitely - and when the lights did eventually go green after 45 minutes, few drivers rushed to venture out.
He said: "My run with the soft tyres was good but with the supersoft I didn't really gain any grip".
"So the main thing for me is to understand the SuperSoft performance".
The Japanese Grand Prix gets underway at 6am United Kingdom time on Sunday.
He told The Guardian: "I've got to make sure I'm fit, healthy, focused".
"So it was something of a blessing when we managed to get a largely dry FP1".
But it meant an action-filled session at one of the world's great race tracks, and some near misses for other drivers in addition to Sainz's accident.
"Our championships in the past three years have come because we have never taken success for granted and, even in the good times, we were able to put our finger in the wound and work on our weaknesses".