Hamilton said he might have taken pole had his last lap not been stopped by Daniil Kvyat’s crash.
Mercifully, the Russian reported over the team radio that he was “okay”, but the session was immediately red flagged, and with less than one minute remaining, did not restart.
Behind the Mercedes’, Bottas took third place for Williams, followed by last week’s victor, Sebastian Vettel, in the Ferrari, with Massa and Raikkonen making up row three. His vehicle was launched into the air and completed a 360 degree spin before it landed upright.
With memories of Frenchman Jules Bianchi’s fatal crash at a wet Suzuka previous year certain to make Sunday’s race an emotional one drivers were anxious to avoid taking any risks in the similarly treacherous conditions.
His Red Bull rolled in the air, after he touched the grass on entry at Turn 10.
Indeed, both Williams drivers had particularly hairy moments when they became the first to venture out on the intermediate tyres.
Their answer was an emphatic one. At the start of the top-ten shootout Rosberg pipped Hamilton by 0.07s, with the world champion hampered by a mistake at the hairpin which saw him lock up and run deep.
That meant Rosberg’s initial time – just eight hundredths of a second better than Hamilton’s poor lap – stood for pole.
Rosberg had his first pole position for almost five months.
Vettel, now 49 points adrift of Hamilton after winning in Singapore, was seven tenths down on the Mercedes pair in fourth.
The session shook itself out and left Jenson Button, who considers Japan his second home race, in P16 and out, just behind teammate Alonso, who snuck through to the second session.
It was the first time in his 14-race career that Sainz had led a session, while Renault had the rare accolade of seeing their engines top the times in both. “Without the yellow flag I’d probably have made it”. “It was a shame we didn’t get to finish the last lap but I’m glad (Kvyat) is safe”.
“To be honest, for us with our downforce it’s not too bad”, he said. Pastor Maldonado was thirteenth for Lotus, while Fernando Alonso managed fourteenth for the McLaren team.
“The auto did not look great so I will be supporting them tonight”.
For McLaren and Honda it never rains but it pours.
Hamilton will head into Sundays’ race with a 41-point margin over Rosberg.
Kvyat’s Red Bull team-mate Daniel Ricciardo, who qualified seventh, added: “It was spectacular and got everyone talking, but it is good he is okay. Obviously he knew he was on the edge, but I don’t think he expected to be on the grass”. I come here to do a job and I am fully aware that despite the success we have had you can’t win them all. It’s a great day today.