Hamilton's 61st career win, and his eighth of the season, came as he converted pole into an early lead, while second-placed Vettel began to drop back immediately.
There were signs that all was not well with the German driver's car when it was seen on the grid with its engine cover off, as the Ferrari mechanics checked for a potential spark plug problem.
Verstappen, who passed Red Bull teammate Daniel Ricciardo off the line, picked off Vettel at the hairpin on the opening lap, before the Ferrari dropped another three places along the start/finish straight at the start of the second tour.
After a brief safety car period, caused by Carlos Sainz crashing his Toro Rosso at Turn 6, Vettel slumped to eighth before getting the call on the radio to pit and retire the car on lap 4.
Hamilton at this stage held a small lead of 1.3 seconds over Verstappen, although by lap 10 this was out to 2.8s and then 4.1s after another five laps.
Verstappen pitted to change his supersofts for softs on lap 21, with Hamilton following suit the next lap, the gap between the pair dropping to 1.8s as Ricciardo took over the lead.
The Australian stopped on lap 25, handing the lead to Valtteri Bottas, who started on soft tyres.
Bottas began to hold up Mercedes teammate Hamilton, allowing Verstappen to close with in a second of his rival, but the gap grew once more when Bottas allowed Hamilton through at the Casio Triangle on lap 28 and started to hold up Verstappen.
It wasn't until lap 30 that Bottas pitted for supersofts, by which time Verstappen had fallen 3.4s adrift.
The Dutchman managed to cut Hamilton's advantage to a little over two seconds in the ensuing laps, but couldn't keep up the pace until Hamilton found himself impeded by Fernando Alonso on lap 51.
That allowed Verstappen to close to within 0.8s at the start of the final lap, but more traffic helped Hamilton escape once more and seal the win by 1.2s.
Ricciardo completed the podium in third, 9.6s behind Hamilton and 0.9s ahead of Bottas, who set a succession of fastest laps on supersofts late on but couldn't quite close down the Red Bull driver.
In the sole surviving Ferrari, Kimi Raikkonen finished fifth, recovering after dropping to 15th on the opening lap, the result of being forced wide at Spoon by Nico Hulkenberg.
The Force Indias of Esteban Ocon and Sergio Perez finished sixth and seventh. A fast-starting Ocon had run as high as third early on after passing Ricciardo on the opening lap, but was soon demoted to fifth on successive laps by Ricciardo and Bottas.
Raikkonen then rejoined ahead of the Frenchman after making a relatively late stop on lap 28.
An aggressive late move at Turn 1 on the Williams of Felipe Massa gave Kevin Magnussen eighth place, with Haas teammate Romain Grosjean following through to grab ninth.
Nico Hulkenberg, another late stopper, was also in this group before the DRS on his Renault got stuck open and he was forced to pit and retire.
Fernando Alonso finished 11th in the final home race for Honda as engine partner to McLaren, ahead of Renault's Jolyon Palmer and Toro Rosso's Pierre Gasly.
Stoffel Vandoorne came home 14th in the second McLaren after dropping to the rear on the first lap.
Sauber's Pascal Wehrlein was the only other finisher in 15th, his teammate Marcus Ericsson crashing out of the race on the eighth lap at Degner 2.
Lance Stroll was also forced out when an apparent failure on the front-right of his Williams sent him skating across the gravel and into retirement in the closing stages.
With four grands prix and 100 points left up for grabs, Hamilton's lead over Vettel is now up to 59 - with teammate Bottas just a further 13 points adrift of the German.
06- 08 Oct 2017 Suzuka International Racing Course, Suzuka
1 | 44 | Lewis Hamilton | MERCEDES | 53 | 1:27:31.194 | 25 |
2 | 33 | Max Verstappen | RED BULL RACING TAG HEUER | 53 | +1.211s | 18 |
3 | 3 | Daniel Ricciardo | RED BULL RACING TAG HEUER | 53 | +9.679s | 15 |
4 | 77 | Valtteri Bottas | MERCEDES | 53 | +10.580s | 12 |
5 | 7 | Kimi Räikkönen | FERRARI | 53 | +32.622s | 10 |
6 | 31 | Esteban Ocon | FORCE INDIA MERCEDES | 53 | +67.788s | 8 |
7 | 11 | Sergio Perez | FORCE INDIA MERCEDES | 53 | +71.424s | 6 |
8 | 20 | Kevin Magnussen | HAAS FERRARI | 53 | +88.953s | 4 |
9 | 8 | Romain Grosjean | HAAS FERRARI | 53 | +89.883s | 2 |
10 | 19 | Felipe Massa | WILLIAMS MERCEDES | 52 | +1 lap | 1 |
11 | 14 | Fernando Alonso | MCLAREN HONDA | 52 | +1 lap | 0 |
12 | 30 | Jolyon Palmer | RENAULT | 52 | +1 lap | 0 |
13 | 10 | Pierre Gasly | TORO ROSSO | 52 | +1 lap | 0 |
14 | 2 | Stoffel Vandoorne | MCLAREN HONDA | 52 | +1 lap | 0 |
15 | 94 | Pascal Wehrlein | SAUBER FERRARI | 51 | +2 laps | 0 |
NC | 18 | Lance Stroll | WILLIAMS MERCEDES | 45 | DNF | 0 |
NC | 27 | Nico Hulkenberg | RENAULT | 40 | DNF | 0 |
NC | 9 | Marcus Ericsson | SAUBER FERRARI | 7 | DNF | 0 |
NC | 5 | Sebastian Vettel | FERRARI | 4 | DNF | 0 |
NC | 55 | Carlos Sainz | TORO ROSSO | 0 | DNF | 0 |
1 | Lewis Hamilton | GBR | MERCEDES | 306 |
2 | Sebastian Vettel | GER | FERRARI | 247 |
3 | Valtteri Bottas | FIN | MERCEDES | 234 |
4 | Daniel Ricciardo | AUS | RED BULL RACING TAG HEUER | 192 |
5 | Kimi Räikkönen | FIN | FERRARI | 148 |
6 | Max Verstappen | NED | RED BULL RACING TAG HEUER | 111 |
7 | Sergio Perez | MEX | FORCE INDIA MERCEDES | 82 |
8 | Esteban Ocon | FRA | FORCE INDIA MERCEDES | 65 |
9 | Carlos Sainz | ESP | TORO ROSSO | 48 |
10 | Nico Hulkenberg | GER | RENAULT | 34 |
11 | Felipe Massa | BRA | WILLIAMS MERCEDES | 34 |
12 | Lance Stroll | CAN | WILLIAMS MERCEDES | 32 |
13 | Romain Grosjean | FRA | HAAS FERRARI | 28 |
14 | Kevin Magnussen | DEN | HAAS FERRARI | 15 |
15 | Stoffel Vandoorne | BEL | MCLAREN HONDA | 13 |
16 | Fernando Alonso | ESP | MCLAREN HONDA | 10 |
17 | Jolyon Palmer | GBR | RENAULT | 8 |
18 | Pascal Wehrlein | GER | SAUBER FERRARI | 5 |
19 | Daniil Kvyat | RUS | TORO ROSSO | 4 |
20 | Marcus Ericsson | SWE | SAUBER FERRARI | 0 |
21 | Antonio Giovinazzi | ITA | SAUBER FERRARI | 0 |
22 | Pierre Gasly | FRA | TORO ROSSO | 0 |
1 | MERCEDES | 540 |
2 | FERRARI | 395 |
3 | RED BULL RACING TAG HEUER | 303 |
4 | FORCE INDIA MERCEDES | 147 |
5 | WILLIAMS MERCEDES | 66 |
6 | TORO ROSSO | 52 |
7 | HAAS FERRARI | 43 |
8 | RENAULT | 42 |
9 | MCLAREN HONDA | 23 |
10 | SAUBER FERRARI | 5 |
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