The Ferrari downfall coincides with the appointment of Sebastian Vettel in 2015 after the German won four straight Championships with Red Bull from 2010-13 in a supremely fast vehicle under the guidance of race engineer Adrian Newey.
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. He was up to sixth by the third corner, passing both Toro Rosso, then fifth when he passed Romain Grosjean's Haas into Spoon.
A rampant Hamilton, who stormed to a record-extending 80th pole, could not resist a dig at his rival. Hamilton however has simply gone from strength to strength and once again in Japan demonstrated why the championship is now in his hands.
The win at Suzuka has left Hamilton with a 67-point advantage over Vettel having been 17 clear just four races ago, and the defending champion suggested Ferrari has taken a step backward rather than Mercedes finding major gains over the past few rounds.
However, the rain ultimately held off until later in the session meaning Vettel had to drive back to the pits for slicks only for it to start raining halfway round his quick lap.
"When we got to midseason we got that win going into the break and then again, really pushing to make sure that we come back even stronger so again, set the bar high".
Knowing Verstappen was carrying a penalty, Vettel still chose to go for an ambitious lunge on the Dutchman into the high-speed Spoon corner.
Verstappen was subsequently given a five-second penalty for not returning to the track safely. Hamilton's team-mate Valtteri Bottas completed a strong one-two for Mercedes.
Vettel's second half of the championship has shaken up his title aspirations. I wasn't desperate to get past.
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"I got through the whole field without any trouble".
Verstappen saw it differently, sniffing: "He could have been a bit more careful".
Verstappen locked up entering the final corner on the opening lap and ran off track, bounced over the grass and kerb as he rejoined at the second part of the chicane.
As a season that began with such promise appeared to be on the brink of collapse, Vettel admitted Ferrari had been under pressure to come up with something special at Suzuka.
That gap shrank to 18.8s at the flag as Ferrari opted not to switch the drivers, denying Vettel an extra two points. I think at least a podium was in our hands today and the vehicle was going quite well.
"And he chose to go around the outside, he could have waited for me to understeer wide".
"He knew that I was there and he just drove into me and pushed me off the track".
The "Prancing Horse" hasn't been helped by reports that Team Principal Maurizio Arrivabene could be moving on to Juventus at the end of this season, meaning that a new boss could enter a jaded Ferrari setup.