Vettel's frustrating 2014 continued on Saturday as he just missed out on reaching the third qualifying period (Q3), forced to settle for 11th after a best lap of one minute and 34.985 seconds.
Red Bull have had a mixed start to the year with Vettel retiring early at the Australian GP before his team-mate Daniel Ricciardo finished second only to be disqualified for a fuel-flow infringement in Melbourne, while in Malaysia, the former finished third but the latter retired with seven laps remaining.
Ricciardo claimed third in qualifying in Bahrain but, due to a grid penalty sustained in Malaysia for a pit-lane violation, the young Australian will start in 13th, while Vettel moved up to 10th.
The four-time world champion bemoaned a lack of speed after qualifying and speculated the problem came about after getting into some gravel during the third practice session.
"We weren't quick enough today. I was pretty happy yesterday, but I think this morning didn't help us when I spun off and did some damage to the car," Vettel said.
"It's hard to say how big the impact of that was, as once you start qualifying you just get your head down and try to do the best you can.
"It was quite tight with Kimi (in Q2) and there wasn't a lot missing to get to Q3 but that's how it goes."
Mercedes again dominated qualifying with Nico Rosberg (1:33.18) taking pole position ahead of team-mate Lewis Hamilton (1:33.464).
Vettel remained confident, however, that he would be able to move up through the field during Sunday's race.
"I think in the race things will calm down and we'll be able to be a bit more consistent and attack for some good points," the Red Bull driver said.
"I think our speed is okay on a longer run – and actually on a shorter run too, as Dan has shown today."
The man who pipped Vettel for a spot in Q3, Ferrari's Kimi Raikkonen, ended up taking sixth spot with a time of 1:34:368 and the Finn said he could see improvement in his Ferrari.
"I am reasonably pleased with my qualifying, because up until this morning, I did not feel completely comfortable in the car," the 34-year-old said.
"But the faith I put in what we had at our disposal was paid back with this result. We are improving in all areas, on the engine, data acquisition, electronics and the new parts fitted to the car have given me a better feeling from the front end."
Williams had shown some good speed in Friday's practice despite completing fewer laps than most of their rivals and their young Finnish driver Valtteri Bottas (1:34.247) proved that was not a fluke as he qualified fourth fastest.
The 24-year-old will start third on the grid after Ricciardo's penalty and was full of praise for his team and his car after qualifying at the Bahrain International Circuit.
"I think we got the maximum potential out of the car today," Bottas said.
"After the Red Bull penalty we are third and after the last two races it's good to see the full potential of the car on a Saturday.
"We haven't done too many laps this weekend so there are things we can still improve for the race, but if we get the strategy right and take the opportunities that come our way we should be in for a good result."