The pole was the 95th of Hamilton's career and seventh in nine races this season, continuing Mercedes' 100% record in qualifying.
Hamilton is seven points clear of Finnish team mate Valtteri Bottas after five of the 21 races.
Lewis Hamilton led a Mercedes 1-2 at the top of the timesheets for the first free practice session at the season-opening Australian Grand Prix on Friday, while McLaren's hopes of a clean start were tempered by reliability issues.
After pipping Ferrari's Sebastian Vettel with a lap of one minute 23.599 seconds in the first practice, the Briton shaved almost a second in FP2, his quickest lap clocked at 1:22.60.
Lewis Hamilton won a thrilling Italian Grand Prix for Mercedes on Sunday to stretch his championship lead to 30 points over Ferrari's Sebastian Vettel, who fought back to fourth after a first lap spin.
The pole was the 91st of Lewis Hamilton's career and seventh at Silverstone.
Lewis Hamilton, the sport's most successful driver of all time and badly affected by the outcome after leading until seven corners from the end, did not attend Thursday night's gala awards ceremony-- a requirement for the championship's top three.
Qualifying took place at a sunny Suzuka on Sunday morning after being postponed from its usual Saturday slot due to the approach of Typhoon Hagibis.
Australian Daniel Ricciardo won the Chinese Grand Prix for Red Bull on Sunday while Ferrari's championship leader Sebastian Vettel finished only eighth.
Daniel Ricciardo is ready for tears, and maybe a few celebratory beers, as the cheerful Australian gears up for his 100th and last race with Red Bull in Abu Dhabi on Sunday.
The clock is ticking for some of Formula One's big name drivers, with world champions and race winners out of contract at the end of the season and a restless young generation eager to take their places.
Formula One's 10 teams will be limited to a maximum 80 people each at races held without spectators when the delayed season gets going in July. Formula One is hoping to start racing behind closed doors in Austria in early July, followed by a number of races in similar conditions elsewhere in Europe.
German Nico Rosberg eased to victory in a chaotic Belgian Formula One Grand Prix on Sunday.
'Just the fact that people have mentioned it, it's already an honour, but it's not been something that I've been chasing in my life'
The four-time world champion's fifth win of the season for Mercedes left him on 213 points to 189 for Ferrari's Sebastian Vettel, who finished second, and relishing the prospect of a stress-free family holiday.
World champion Lewis Hamilton splashed through the puddles at a rain-soaked Sepang International Circuit to secure pole position for Mercedes in a hectic Malaysian Grand Prix qualifying session on Saturday.
Sports bodies moved quickly to strip Russia of events,
The 21-year-old is the first Ferrari driver since seven times champion Michael Schumacher to take four consecutive poles in a single season.
Nico Rosberg won the Austrian Formula One Grand Prix for the second year in a row in a Mercedes one-two finish with team mate Lewis Hamilton on Sunday.
Red Bull have given "a definite no" to four-times Formula One world champion Sebastian Vettel's hopes of returning to them next year, team boss Christian Horner said on Friday. The German, who is out of contract with Ferrari at the end of the season and facing an uncertain future, had said on Thursday he would say yes to a Red Bull drive if one was offered.
Mercedes were summoned by stewards post-race for the infringement.
'I don't feel like I'm at the end. The next eight months or so I'll find out whether I'm ready to stop or not, I don't think I will personally, but you never know.'
The Briton had won his own fifth championship in Mexico two weeks previously but the broader celebrations were kept in check until Interlagos.
Lewis Hamilton seized pole position in the dying seconds of qualifying for the first Portuguese Grand Prix in 24 years on Saturday to deny and dismay Mercedes team mate Valtteri Bottas once again.
Three-time world champion Lewis Hamilton dominated practice at the season-opening Australian Grand Prix on Friday, putting Mercedes on top of the timesheets and leaving his Formula One rivals with plenty to ponder before the weekend.
Seven-time world champion Lewis Hamilton will be staying in Formula One for the next two years at least after he and Mercedes announced a contract extension on Saturday.
Nico Rosberg had his Formula One world championship lead over Mercedes teammate Lewis Hamilton cut to one point after the German was demoted from second to third place in the British Grand Prix on Sunday.
Champions Mercedes are chasing a sixth successive double, and Lewis Hamilton his sixth drivers' title, but the task looks tougher than ever.
Hamilton held off a mid-race challenge from Red Bull's Max Verstappen to register a record-equalling fourth triumph at the floodlit Marina Bay Street Circuit track, while Vettel finished third to slip further behind in the title race.
Ferrari's Sebastian Vettel, winner of 52 races, has gone more than a year since he tasted victory at last year's Belgian race.
Hamilton has won half of the season's 20 races so far, propelling his team to an unprecedented sixth successive title double, but Brazil was a disappointing weekend with Valtteri Bottas retiring.
Formula One has said it hopes to get the season started some time in the European summer with a reduced calendar of 15-18 races.
Britain's Lewis Hamilton eased his Mercedes to a dominant victory in the German Formula One Grand Prix on Sunday and secured his fourth victory in a row.
Sebastian Vettel's Formula One title bid could suffer a further setback after a bizarre post-race incident at the Malaysian Grand Prix on Sunday.
IMAGES from the Silverstone F1 GP on Sunday
The race has been won from pole eight times out of 11 editions.
Lewis Hamilton surpassed Ayrton Senna's career haul of 65 pole positions in Formula One as he edged Mercedes team mate Valtteri Bottas to secure top spot the Azerbaijan Grand Prix on Saturday.
Lewis Hamilton is on course for his most successful campaign yet and can become only the third driver after Michael Schumacher and Sebastian Vettel to win 13 times in a season.
Formula One world champion Lewis Hamilton took pole for Mercedes at the season-opening Australian Grand Prix.
Lewis Hamilton took pole position at the Italian Grand Prix for the third year in a row on Saturday with Mercedes team mate and title rival Nico Rosberg joining the Briton on the front row of the grid.
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