However, rain and gusting winds from a passing typhoon are set to make the fast-flowing Suzuka circuit even trickier for drivers in qualifying.
Hamilton, who leads Vettel by 50 points with just five races left this season, will be hot favourite to take pole after also dominating practice on Friday, when he went 1.3 seconds faster, albeit on a dry track.
Daniel Ricciardo carries an image of a Honey Badger on his helmet because he identifies with the animal's strength, ferocity and fearlessness.
He said that lap would have been "sort of OK" without the error.
Vettel's hopes of challenging the Briton were wiped away when he looked to dive down the inside of Verstappen at Spoon but connected with the Red Bull and both cars went off track. But while the team will be disappointed they can still take some consolation from both cars finishing ahead of Honda's former chassis partner McLaren. Although it wasn't penalised by the stewards, his chop across the Sauber must have been as close to the limit as you can get without receiving a time penalty of some sort.
Haas trimmed Renault's advantage in the constructors' championship to 11 points in Russian Federation, but they could nearly erase the deficit altogether with a strong result in Suzuka.
Hulkenberg was, along with teammate Sainz and Perez, one of three drivers not to have set a time at that point, and after going out immediately after the restart was relegated into the drop zone by a flurry of improvements as Q1 was chequered-flagged.
Overtake of the race: Just a few laps before his botched overtake on Verstappen, Vettel pulled a remarkable move on Romain Grosjean on the straight down to Spoon with two wheels on the grass.
As pointed out earlier, overtaking is hard at Suzuka and if the two Toro Rossos can get away cleanly then they will have a good chance of a double-points finish.
Vettel has a storming opening lap, climbing brilliantly into fourth.
Many eyes were on the skies during qualifying on Saturday, with rain hitting the end of Q2 and again during Q3.
It appears to be an advantage given the fact that the soft will last longer into the race and does not suffer as much degradation as the supersoft, but there are always downsides.
Despite only a smattering of raindrops in the moments before the shootout for pole, Ferrari elected to put Vettel on wet tyres. Max Verstappen (NED) Red Bull-TAG Heuer 1:29.057 4. Down the order Vettel is 15th after pitting.
When Verstappen was asked whether or not he would want to get in the way of the driver championship battle between Hamilton and Vettel and the constructor championship battle between Mercedes and Ferrari if Raikkonen and/or Vettel are able to catch up to him in tomorrow's race, the 21-year-old Dutchman threw shade at Vettel and Ferrari.