Ferrari had both cars on the podium with Kimi Raikkonen in third, while Mercedes' second driver Valtteri Bottas had to settle for eighth in Australia, following a qualifying crash and grid penalty. Hamilton ended up second because his team made an error of judgment during Vettel's pitstop.
Vettel came closest, posting a time of 1:29:828 on a qualifying simulation lap while Bottas was half a second further back in third.
His hopes of chalking a 3rd Bahrain win on Sunday have been taken a hit, with all the Briton place to shed five puts on the grid for the unscheduled gearbox change in his Mercedes.
"Overall I have been happier this weekend with how the vehicle has been responding and how the front end is responding". "Ferrari have done a great job this weekend, they've got the pace and it's been a hard weekend for me overall in general".
Lewis Hamilton says Mercedes' failure to out-qualify either Ferrari in Bahrain shows speculation about the team's so-called "party mode" engine setting has been overblown. "The vehicle was excellent all weekend so far".
Back-to-back wins would boost Ferrari in their bid for a first place title since 2007, but with 19 races to follow, they won't get carried away, after Vettel led early last season but Hamilton eventually took the title.
Lewis Hamilton, who travelled in to the weekend favorite for victory after noticed it sailed off by an illtimed digital safety vehicle two weeks ago at the season-opener at Melbourne, was just fourth fastest, 0.823 minutes away Raikkonen's most useful. Here the track improves all the time, with more grip every lap.
"But after the weekend, after the race distance, when you have so many laps - I had a very good understanding and feel, and we have been talking about it and looking into it". I know exactly what I want, and we need to work on it.