Bottas, who has not won this year, was.044 seconds quicker in his Mercedes than Red Bull driver Max Verstappen on the Yas Marina circuit.
Red Bull driver Daniel Ricciardo was third fastest in the second practice, followed by Hamilton.
He will be joined on the 2019 grid by Britain's George Russell, who will make his debut for Williams as the GP2 champion after winning the feature race at Abu Dhabi to seal the title in his rookie year. "My goal for the weekend is to repeat last year's result".
For the second straight year, four-time F1 champion Vettel led during the championship - and was close behind Hamilton at the halfway stage.
Sunday's race begins at 5:10 p.m. local time (1310 GMT) and ends under floodlights.
"There is a big step, maybe one second between the ultra and the hyper so we needed to do more or less the ideal lap on the ultra to make it through Q2". As his first stint in Brazil showed, Verstappen can make his tyres last early in a race, so he won't be seeing the different strategy as something that will stop him mixing it with the rest of the front runners.More news: Kante signs five-year deal with Chelsea
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He said: "We're doing Indianapolis together, we'd like him to be part of our racing programme because we're also reviewing other forms of motorsport, which has been widely noted - World Endurance, a full season of IndyCar - and he's certainly not done driving". "There's a big difference in track temperature between the two sessions".
"And then with the engineers and just helping us all work together to understand what next year's auto is doing, what the feedback is from the drivers, and what would Fernando do in a certain situation - that experience will be very valuable to us". "I felt positive right from the start".
Sauber have only scored at least that many points in two races this season - in Azerbaijan and Mexico - but this is a team that will finish the season without going two races without scoring for the first time since 2008.
"Since Monaco I've been hoping for a strong weekend and now this is my last chance with the team".
"It's a much smaller team than where I've been now, at Ferrari, but I'm really looking forward to it".
"We have solid race pace and hopefully our degradation will be better than Ferrari and Mercedes and we can apply the pressure". He executed nearly perfectly, especially in the final sector, and could not be matched, although Sebastian Vettel (who was third) and Bottas clearly gave their all.