Hamilton recovered to second, beating Raikkonen, but referred to "interesting tactics" from Ferrari on the podium and Mercedes team principal Toto Wolff said they had questioned whether the incident was "deliberate or incompetence".
The safety auto was then deployed for a big crash, which ended Marcus Ericsson's race.
He was soon up to 16th and by lap nine he was eighth, but some distance from Vettel, who led Bottas by six seconds on lap 12.
Hamilton rushed back into the mix for a podium spot with the majority of runners picking a one-stop strategy until Marcus Ericsson lost control of his Sauber at Turn 1, and his fierce shunt into the tyre barrier brought out a lap 33 safety vehicle.
"Obviously I was pretty happy with the first run in Q3 and then we had a little bit more in sector three and bits around the track, which I think I got right on the second attempt, but I seemed to lose a little bit down the straights".
Raikkonen, who accepted full responsibility for the contact, was handed a 10-second time penalty and went on to classify third, while Hamilton recovered from the rear of the pack to take second, behind victor Vettel.
But the headlines belong to Vettel, who suffered a neck injury during practice on Saturday and was forced to wear supportive tape during the race, but came through for his fourth win of the season. Especially here because I mean, here is not easy.
"It was my mistake", he said.
Vettel was first to clock a track record and it kept falling as drivers took advantage of soft tires on the new asphalt track. "You are the fastest by miles, so don't give up". A number of times Vettel attacked at Brooklands after using DRS, and Bottas repelled, with Hamilton similarly fighting Raikkonen but also filling Vettel's mirrors.
It was not to be for Lewis Hamilton.
"Now he will have to get his head down, he has 13 seconds of clear space and then has Ricciardo, Raikkonen and Verstappen and that is when it will get a lot harder". Lance Stroll (CAN/Williams) 38.106, 14.
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