Ferrari had detected a spark plug issue on the way to the grid and removed the engine cover from vehicle No.5 in an attempt to rectify the problem before the start.
Vettel lost a place to Max Verstappen at the hairpin before slipping all the way back to sixth on the main straight, with yet more positions being lost after a brief safety auto period.
The current result places Hamilton in the title lead with a total of 306 points, 59 points clear off Vettel who is second with a total of 247 points.
Hamilton can clinch the title in the next race. I was excited actually to have a good race with Sebastian here, as I was in the last race, but he's obviously been incredibly unfortunate.
"I don't honestly think there is anything wrong with the engine, I just felt a couple of things", he said.
LEWIS HAMILTON dominated on the track but was outsmarted off it by joker Daniel Ricciardo.
"Of course it hurts, and we're all disappointed", said the four times world champion, who hugged his mechanics and gave the crowd a quick wave after returning to the pits.More news: Jaguars vs. Steelers Point Spread: NFL Week 5 Odds, Prediction
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The formation lap went smooth, and soon as the lights went out Hamilton managed to hold Vettel off, the two were followed by Ricciardo and Verstappen.
Vettel's emotions unsurprisingly were rather different: "I think I need to protect them", he told Sky Sports F1.
"For me, there was not a lot [discussion], maybe internally there was more", Bottas said. The race after the start spread out and it wasn't that exciting from my point of view.
Race victor Lewis Hamilton: "We have had such a great crowd this week you always look after us so well and the support was vast".
Ricciardo took third place, a further eight seconds back, while Bottas recovered from his gearbox penalty on Saturday to finish fourth.
Late for the anthem, the German also had little to say to the waiting media before departing the circuit early.
"It's a circuit I've always enjoyed, and with this year's auto it's a lot of fun".
Kimi Raikkonen, who will also drop five places on the grid for an unscheduled gearbox change after a crash in Saturday morning's final practice session, set the sixth fastest time. Brazilian Felipe Massa rounded out the top 10 for Williams. Esteban Ocon ended the race in sixth spot ahead of his Force India teammate Sergio Perez to win a closely fought encounter, with the latter finishing seventh.