Shock: From the very first session of Friday practice, it seemed unlikely Ferrari would challenge Mercedes for victory in Suzuka but nobody expected the fastest red vehicle to be 50 seconds off at the finish.
The Briton now has a 67-point lead over Vettel with four races remaining and can sew up the championship next week with victory in Austin should the German finish lower than second.
Bottas dropped back from Hamilton and Verstappen was soon on Bottas' tail but although he pressured the Finn to the end, the Red Bull driver could not get through.
"If I don't go for that gap and that gap was there, I might as well go home".
Ferrari's Sebastian Vettel was in the wrong against Max Verstappen.
"Of course we didn't spin off the track [like in China], but he drove into the side of my vehicle".
"In that corner you can't overtake", shrugged the Dutchman, who had earlier received a five-second penalty for nudging Raikkonen off the track.
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"Initially in the race, everything felt good". His first was at Canada in 2007, one year after Michael Schumacher secured the last of his 68 poles Paper boy: Vettel's helmet design incorporates origami "Ah, see you went for the furry heart with photo pocket option, too".
Verstappen continued without losing much time but Vettel spun to the back of the field and was now consigned to a long afternoon fighting back. Races like this are a bit of a hand-over and we know it is hard from where we are in the point standings, but we don't have much to lose. The stewards investigated the incident, but tellingly took no action.
Vettel's championship hopes hang on by a thread as the German driver made another crucial mistake that has affected the gap to championship leader Lewis Hamilton.
Esteban Ocon completed a double points finish for Force India in ninth while Carlos Sainz took the final point for Renault.
"I think we expected that there was more rain coming and obviously it didn't".
Indeed, the move smelt of desperation, and it marked Vettel's second mistake of the weekend, after he ran off track in qualifying, and his seventh of an error-prone campaign.
"I got through the whole field without any trouble", added the former world champion. "But I don't think there was an very bad big gap".
"He knew that I was there and he just drove into me and pushed me off the track".
Ferrari boss Maurizio Arrivabene said the podium had been within the team's grasp.