Red Bull driver Max Verstappen of the Netherlands was second and Mercedes driver Lewis Hamilton, right, of Britain third.
"First of all, I don't know any of these things", Rosberg said when quizzed on Hamilton's attitude in Japan. "The Stewards are conducting a hearing".
"Max moved when under-braking", complained the Brit - and it now appears that Mercedes are intent on sealing a belated one-two in Suzuka by alleging that Verstappen drove "erratically and in a risky manner".
The 19-year-old remained within about five seconds of race victor Nico Rosberg throughout the race but the German, who extended his championship lead over team-mate Lewis Hamilton to 33 points, was in total control throughout.
In fact, rather than believing that Hamilton's mind was elsewhere, Rosberg said all he had noticed was a new-found determination from the world champion to get the job done. There are four weekends to go, and Lewis will regroup.
"No stress, Lewis", came the reply before Hamilton began a rousing charge through the field to make up places. "He was working the longest hours I have seen him work in many months trying to get the little extra bit of lap time".
Vettel and Raikkonen were fourth and fifth respectively, with Ricciardo, the victor in Malaysia last weekend, a distant sixth.
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Those states, as well as North Carolina, declared states of emergency, empowering their governors to mobilize the National Guard. Augustine flooded even as the hurricane was still approaching. "The flooding is just going to get higher and higher and higher".
"I saw him moving and as soon as I saw that I closed the door, and I think he was far enough that he could see I was going to do that".
"Max moved under braking, " Hamilton complained, and his Mercedes team subsequently lodged a protest against the Dutch teenager, the outcome of which will be ruled on at the United States Grand Prix on Thursday. The win, Rosberg's fourth of the last five races, ensures that he now has a total of 313 points, while Hamilton has 280 points.
The Mercedes chief has also backed the Briton to take his title fight with Nico Rosberg down to the wire.
With Hamilton closing in on Verstappen he tried to overtake at the chicane on the penultimate lap and had to avoid the Red Bull as he ran wide due to Verstappen's defence.
The world champion said: "That's a healthy margin for Nico".
Daniel Ricciardo, victor in Malaysia a week ago, was sixth in his Red Bull as Force India pulled further ahead of Williams in their private battle for fourth overall. "I lost a lot of ground and had to fight back and I'm happy that I did so and got it back".
Seventh and eighth place went to Force India Mercedes' Sergio Perez and Nico Hulkenberg respectively, ahead of their Williams rivals Felipe Massa and Valtteri Bottas who completed the top ten.