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The four-time champion German delivered a best lap in one minute and 28.846 seconds to outpace his new Monegasque partner by 0.035 seconds at the top of the time-lists, the pair winding up six-tenths clear of Lewis Hamilton.
"From the team's point of view, I hope Melbourne was a one-off," said a relieved and newly-moustachioed Vettel.
"I really like the car in winter testing and it wasn't there in Australia so I am hoping this is it again."
Hamilton, the defending five-time world champion, was unable to match Ferrari's pace in his Mercedes as he took third ahead of team-mate Valtteri Bottas, winner of the season-opening Australian Grand Prix.
"It's hard work out there for everyone," said Hamilton.
"First practice was incredibly hot, the track is at 50 degrees, so everyone is struggling with the tyres. The Ferraris have been quick from the get-go and picked up more pace from there so it's completely different to Melbourne.
"We had some issues with the balance of the car, but we've made improvements. It looks like the Ferraris are ahead, so we have to keep our heads down, keep working, analyse things and try and come back stronger.
"I think it will get a little bit closer, but it is going to be a tough battle."
Bottas said: "The car balance didn't feel great in the first session, but we made some changes and the car felt much better. It looks like it's going to be very close between us and Ferrari.
"They are clearly faster around here than they were in Melbourne. So we will have some work to do to improve the set-up."
In the 999th Grand Prix meeting in the history of the Formula One world championship, Vettel's form also endorsed the speed delivered by Ferrari when they finished first and second in the opening session, led by Leclerc.
Vettel, who has taken pole three times before at the Sakhir circuit, is seeking to become the first driver to win three Bahrain races in succession.
But Mercedes boss Toto Wolff warned that Hamilton's threat should not be ignored.
"I think it's always dangerous to underestimate Lewis Hamilton. He's always there and Valtteri Bottas has started off where he left off in Melbourne.
"It looks like Ferrari has a tiny edge on us, but we'll squeeze everything we can like a lemon!"
Vettel's fellow-German Nico Hulkenberg was an encouraging fifth for Renault ahead of Dutchman Max Verstappen of Red Bull, Dane Kevin Magnussen of Haas and British rookie Lando Norris of McLaren.
Frenchman Romain Grosjean was ninth in the second Haas ahead of Russian Daniil Kvyat for Toro Rosso.
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