The only sour note for Ferrari was the sight of Raikkonen pulling off the track towards the end of the session with a loose front-right wheel, although the Finn escaped a grid penalty.
But Vettel made it count when it mattered.
Mercedes got closer in qualifying than they looked like they might at one point but Vettel was still 0.166 seconds quicker than the fastest Mercedes of Bottas.
Hamilton came to Bahrain knowing he was in for a five-place grid penalty for a gearbox change, so he needed to be on his game - with a flawless auto - to minimise the damage and give himself the best chance in the race.
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.
"Overall I have been happier this weekend with how the auto has been responding and how the front end is responding". Really happy that I got the second run and got it clean.
Kimi Raikkonen said there was nothing he could do about losing pole position to Ferrari teammate Sebastian Vettel in Bahrain after hitting traffic in the closing stages of Q3. It looked like a similar error, just losing control of the vehicle through the apex, at a race Red Bull would have hoped to have two cars putting Ferrari under pressure from the very start.
The British star had wound up fourth fastest earlier in Friday's second free practice session at the Bahrain International Circuit. I know exactly what I want, and we need to work on it.
Raikkonen set the pace with a 1:29.868, leading Red Bull Racing's Max Verstappen by 0.525 seconds, with the Dutchman being his nearest challenger.
"On the softs, the auto were much better, but putting the softer compound on, the supersoft, it looks like we're overheating and therefore not extracting the optimum grip".
Fernando Alonso was 0.313s clear of teammate Stoffel Vandoorne, but that will be little consolation for the two-time champion who was 0.4s off the Honda-powered Toro Rosso of Gasly.
Nico Hulkenberg along with Carlos Sainz place Renault best-of-the-rest with all the eighth and seventh quickest situations.
Such support came as no surprise given their performances on the track, Williams finding it particularly hard as Lance Stroll and Sergey Sirotkin finished FP2 17th and 18th respectively.
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