Kiwi driver Brendon Hartley finished 11th after sitting as high as eighth at one point.
Mercedes' Valtteri Bottas was the fourth-quickest in the session with a time of 1:32.616 minutes.
The stewards' decision, made in wet conditions, had reduced Vettel's slim title chances according to Ferrari team boss Maurizio Arrivabene and means that he can not start on the front row of the grid for a race in which he knows another Mercedes one-two will give Hamilton his fifth drivers' title.
Vettel picked his way through the midfield and up to 10th place by Lap 6, but the victory race was thrown a curveball on Lap 10 when Ricciardo's vehicle switched itself off at Turn 11, forcing him retire by the side of the road and triggering a virtual safety auto.
The costly stop pushed the Briton down to fourth and despite his best efforts, he could not put enough distance between himself and Vettel to wrap up the championship on American soil.
Once rejoining the race, Hamilton queried both the delay and the tyre choice Mercedes made, to take the softs rather than the super-softs Verstappen had taken. Just imagine what Verstappen is going to be able to do when he gets a front-running auto.
He roared past Ricciardo on the back straight, only to go too deep on his brakes, and lose the position. Hamilton now has a 70-point lead with 75 remaining to be won.
Raikkonen drove a superb race.
That gave him the lead and on older tyres he was controlled and flawless in the closing laps as Verstappen and Hamilton applied pressure from behind.
"It was definitely an issue for us and we'll look through it as performance-wise it wasn't a great weekend". Got a good start and needed to push hard.
"We had enough speed and we keep it consistent". We are close and I felt good with the vehicle.
Hamilton started from pole, but lost the lead to Raikkonen on the long uphill race to the left-handed first corner.
Ricciardo's team mate Max Verstappen would also have hoped to be in the mix but the young Dutch driver will start 13th after suffering suspension damage in the first phase of qualifying. "The tires were not in the best shape, but I think they were a bit similar to Max's". I think it's probably the best thing and I wasn't at any point disappointed with the decision.
"Obviously having to answer questions about my future every week which is getting increasingly annoying and I've read in the media that I have to beat my team-mate (Pierre Gasley) and I was ahead in Singapore until team orders, I was ahead in Russian Federation until the auto broke down, I was ahead in Suzuka in qualifying and I was ahead today, so lets see what happens". "We have to do the same work as before". A fifth career title would tie the British driver with Argentina's Juan Manuel Fangio for the second-most championships in Formula One history. But can he beat a revived Ferrari there?
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