Malaysian GP winner Max Verstappen followed Hamilton closely and Daniel Ricciardo on third ahead of Valtteri Bottas.
Hamilton secured his eighth win of the second and third in the last four years at Suzuka to extend his lead over Vettel to 59 points, meaning he can clinch his fourth world title at the next race in Austin, US Grand Prix.
The Brit’s Mercedes also suffered a technical issue and he had to survive a late fright as Dutchman Verstappen closed quickly, but he held on to secure his 61st career victory, his fifth in the last seven races to put him in the box seat in the championship race.
” I could only have dreamed of having this kind of gap,” he said. “Ferrari has put in such a great challenge all year round.”
Unfortunately for Vettel, that challenge has petered out and he cast a dejected figure after his retirement.
“Pity the last two races with reliability issues, but it is like that sometimes,” he admitted.
“We still have a chance this year. We got a lot further than people thought, so there are some positives.”
Kimi Raikkonen finished in the fifth place after managing to fight his way past the Force India pair of Esteban Ocon and Sergio Perez, who secure P6 and P7 respectively.
Haas F1 duo Kevin Magnussen and Romain Grosjean finished eighth and ninth respectively, the pair overtook Felipe Massa late on, the Brazilian took the final point on offer in P10 for Williams.