Raikkonen drifted further away from the Red Bulls in fifth, while Vettel gradually made his way back to sixth - but by the time he was clear of the rest of the field, he was a minute behind Hamilton and 40 seconds behind Raikkonen.
If Hamilton wins the next race, the US Grand Prix in Austin and one of his favourite tracks, the 33-year-old will be champion with three races to spare in case Vettel finishes lower than second. Now it is a matter of just when Hamilton closes it out and equals Juan Manuel Fangio's five F1 titles.
"It's a great one-two for Mercedes and a true showing of the strength in depth we have", said the Briton after his fifth Japan victory and ninth of the season.
Hamilton was leading from pole position.
Having quickly progressed from eighth on the grid following his poor qualifying, Vettel was attacking Verstappen for third at Spoon corner on the first lap after an early safety vehicle at Suzuka when they tangled and the Ferrari spun.
The safety auto was deployed on lap five after Kevin Magnussen left debris on the track after clashing with Charles Leclerc, however when racing resumed on lap eight, Vettel's valiant efforts were promptly wasted.
Vettel tumbled down the order to 19th and while both were investigated by race stewards for the collision, no action was taken. The gap was there, but as soon as he saw me, he defended, but I had the inside.
Ferrari boss Maurizio Arrivabene said the podium had been within Ferrari's grasp.
"After the race start when I was second I kind of knew how the race was going to be", said the Finn after the finish.
Vettel knew he had to make up ground quickly if he was to have any hope of stopping Hamilton's apparently unstoppable march to the title which for a long time looked as if it could be the Ferrari driver's.
Verstappen had already incurred a five-second penalty after nudging Kimi Raikkonen's Ferrari off the track.
"This weekend we were lucky that Ferrari was not challenging us because they did some mistakes", he said. I don't regret the move, obviously with that outcome you would do it differently because with hindsight it's always easy.
The scenario has been set up because Vettel finished sixth at Suzuka after a collision with Max Verstappen, and Hamilton says he was expecting a much tougher challenge from Ferrari and Vettel heading into the summer break.
Frenchman Pierre Gasly, who started seventh on the grid, finished 11th after losing out to Sainz two laps from the end while New Zealander Brendon Hartley, who lined up sixth, fell to 13th at the finish. Out came the safety auto after debris littered the track following a coming together between Kevin Magnussen and Charles Leclerc.
For more sports coverage, visit the ABS-CBN Sports website.