Vettel's total stationary time was 5.6 seconds, dropping him to fourth behind both Bottas and Red Bull Racing's Max Verstappen.
"This is when we're going to start to continue to apply the pressure". "I felt really comfortable in the vehicle". His pole position, taken after a close battle with teammate Valtteri Bottas and Vettel, was greeted with relief.
Unusually for Barcelona, it was a race of attrition with six retirements. He now has 95 points to Vettel's 78 after five rounds of the 21-race championship.
The victory in Spain comes two weeks after Hamilton claimed a fortuitous victory in Azerbaijan where Bottas retired from the lead late on.
Beating Hamilton was never on the cards but Bottas fought hard, overcoming tyre wear (on the medium compounds) to defend track position from Max Verstappen who was breathing on the tail in the final laps.
But Ferrari's misjudgement saw Max Verstappen take advantage - despite an earlier coming together with Lance Stroll (him again) resulting in a virtual safety vehicle - to take his first podium of 2018 for Red Bull.
"We do after the five races now have a much, much better understanding of the vehicle, of what we need to do to get the auto to be working - but we still have learning to do, improvements to be made". Kimi Raikkonen (Ferrari) 48, 5.
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This marks Verstappen's first podium of the 2018 season. The thinner tread on the rubber Pirelli have supplied this weekend in response to the blistering during testing in Barcelona certainly seems to work to their advantage and the same type of tyres will be used at the French and British grands prix. Our ambition needs to be that we're better off rather than worse off.
A chaotic race start saw three drivers taken out in the first lap when Haas' Romain Grosjean took himself, Toro Rosso's Pierre Gasly and Renault's Nico Hulkenberg out of the race before it even started.
"Feels nice to be on the podium and nice to have a good clean race", said Verstappen.
But Red Bull can ill afford a repeat between the highly competitive pair, having insisted they apologise to the entire team after their Baku collision cost them valuable points.
"We definitely go to Monaco on a high note, but we know that we still have a lot of work to do".
Behind the leading four, despite being fast and setting the fastest lap of the race, Daniel Ricciardo brought the second Red Bull home in fifth. Following a safety vehicle appearance, Hamilton got the whole shot on the restart and rabbited away. Sergio Perez (Force India), 10. But racing was immediately interrupted by the safety auto when Nico Hülkenberg and Pierre Gasly were collected by Romain Grosjean in the Haas who went off and spun back across the track through the third corner.