Publications
Partners
World champion Hamilton, who leads the championship standings by 41 points from Rosberg, will start alongside the German at Suzuka on Sunday, while Ferrari's Sebastian Vettel qualified for the second row.
"Happy birthday, mum!" Rosberg said in German after securing only his second pole of the year.
"That's a birthday present for you. At times today I had the perfect car and I pretty much nailed my laps. Obviously it's a great comeback for the team after Singapore."
Finland's Valtteri Bottas steered his Williams to third on the grid ahead of Vettel - who won last weekend's night race to boost his outside title hopes - with team-mate Felipe Massa and Kimi Raikkonen's Ferrari on the third row.
Rosberg also topped the timesheets in a frantic final practice session on Saturday morning after heavy rain effectively washed out Friday's practice.
With memories of Frenchman Jules Bianchi's fatal crash at Suzuka last year raw this weekend, Kvyat reminded everyone of Formula One's inherent risks when he crashed spectacularly on approach to the hairpin.
Despite flipping over and totalling his car, the Russian was able to climb out of the mangled wreckage unhurt as red flags brought a premature end to qualifying.
"I'm okay, and you?" Kvyat chirped over the radio when asked if he had sustained any injuries. He will start the race from the pitlane after his 180kph shunt.
There was early drama when Max Verstappen's Toro Rosso rolled to a halt poking out dangerously across the track after breaking down with electrical trouble, costing him a grid demotion of three places.
The Dutch teenager trudged back to the pits, yellow flags having bounced out several drivers, including Jenson Button, who was furious after his worst ever Japan qualifying result.
"The position we are in, we can't afford to make any mistakes," the Englishman snapped at McLaren mechanics, frustrated by an earlier communication mix-up.
Red Bull's Daniel Ricciardo qualified seventh quickest with Frenchman Romain Grosjean alongside him on the fourth row for the troubled Lotus team, whose Formula One future has been plunged into doubt over a cash-flow crisis.
A repeat of Hamilton's victory in Japan last year, when he was also pipped to pole by Rosberg, would put the Briton tantalisingly close to a third world title with five races left.
"Definitely the car feels like normal this weekend, which is great to see," said Hamilton after narrowly missing out on his 12th pole of the season. "I was enjoying the battle with Nico. It was a shame we didn't get to finish the last lap but I'm glad (Kvyat) is safe."
Vettel, meanwhile, was realistic about Ferrari's chance of inflicting another upset.
"Ideally I would have like another spot (on the grid) but let's not be too greedy," said the German, who ended a run of 23 straight qualifying wins for Mercedes last time out. "We can be reasonably happy.
"The weather could be a challenge tomorrow," added four-time world champion Vettel. "I watched the forecast on (Japanese) TV last night but I couldn't catch a word."
Hamilton suffered his first race-ending retirement in over a year in last Sunday's race, when the dominant Mercedes were rocked by a mysterious loss of pace, but normal service has been resumed in Japan.
He will be chasing an eighth victory of the season in Japan and bidding to equal boyhood hero Ayrton Senna's tally of 41 race wins.
Starting grid for the Japanese Grand Prix after qualifying on Saturday:
1st row
Nico Rosberg (GER/Mercedes)
Lewis Hamilton (GBR/Mercedes)
2nd row
Valtteri Bottas (FIN/Williams)
Sebastian Vettel (GER/Ferrari)
3rd row
Felipe Massa (BRA/Williams)
Kimi Raikkonen (FIN/Ferrari)
4th row
Daniel Ricciardo (AUS/Red Bull)
Romain Grosjean (FRA/Lotus)
5th row
Sergio Perez (MEX/Force India)
Daniil Kvyat (RUS/Red Bull)
6th row
Nico Hulkenberg (GER/Force India)
Carlos Sainz (ESP/Toro Rosso)
7th row
Pastor Maldonado (VEN/Lotus)
Fernando Alonso (ESP/McLaren)
8th row
Max Verstappen (NED/Toro Rosso)
Jenson Button (GBR/McLaren)
9th row
Marcus Ericsson (SWE/Sauber)
Felipe Nasr (BRA/Sauber)
10th row
Will Stevens (GBR/Manor Marussia)
Alexander Rossi (USA/Manor Marussia)
