Ferrari has since been fined 5,000 euros by the FIA for an unsafe release, but Raikkonen avoided a three-place grid penalty.
Despite narrowly missing out on pole Raikkonen has made a strong start to the season, but he says nothing has dramatically changed since previous year, where he struggled to match Vettel across the whole season.
The German, victor previous year on this circuit, lapped the 5.4-km Sakhir track in a time of one minute 27.958 seconds on Saturday, edging Raikkonen by a margin of 0.143 seconds.
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Ferrari have looked to have an edge on Mercedes all weekend, Hamilton and Bottas battling inconsistent handling on the stop-start Sakhir circuit in the desert south of the Bahraini capital Manama.
Hamilton's setback in his bid to overhaul Vettel's early-season lead in the title race - following his victory in the season-opening Australian Grand Prix - was confirmed by the International Motoring Federation (FIA), the sport's ruling body. "First run in Q3 I was very happy and then I tossed it away last corner".
When asked where the pace has gone since Melbourne, he said: "I think that was a really good lap from me and whilst I tried to get the same again here it's not something you can always do". None other than Gasly in the Toro Rosso, who was just 1.371 seconds behind the pole of Vettel.
A Mercedes spokesman confirmed Hamilton would have a new gearbox for final practice and qualifying, incurring an automatic five-place penalty.
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Friday's practice sessions also offered encouraging signs with Raikkonen heading Vettel in a Ferrari one-two at the top of the time-sheets.
But he could only manage fourth, failing to improve his time on his final lap and leapfrogged by Bottas. We tried some things that didn't work which is why the gap was sometimes bigger.
The two Red Bulls of Verstappen and Daniel Ricciardo followed behind in second and third respectively. It looked like we were a bit quicker than the rest but it depends a bit on the programme. Gasly (Toro Rosso), 6.
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Williams completed the bottom of the timing screens, with Sergey Sirotkin 0.419 seconds adrift of Leclerc's Sauber in 19th while Lance Stroll finished as the slowest driver of the session in 20th, nearly three seconds off the pace.