Rosberg opened up a 33-point lead over his Mercedes teammate Lewis Hamilton after the two-time defending champion could only manage third place at Suzuka.
Hamilton, still smarting from the engine blowout which cost him victory last weekend in Malaysia
, made a terrible start as he looked to put pressure on polesitter Rosberg and had to battle hard to even make the podium.
Red Bull's Dutch teenager Max Verstappen took second place with another mature drive to belie his tender years, holding off Hamilton in a tense duel over the closing laps.
Hamilton made his attempted overtaking move on the chicane on lap 52 of 53, but Verstappen was alert and closed him off.
Mercedes later lodged an official appeal over the incident, but it was later withdrawn, apparently at the request of Hamilton, although the team later denied this.
"There is no protest from myself. Just heard the team had but I told them it is not what we do. We are champions, we move on. End of!" Hamilton tweeted.
With only four rounds of the 2016 championship remaining and a maximum of 100 points on offer, Rosberg is now in the box seat in the title race and the German was naturally delighted after wrapping up his ninth win of the season and his first in Japan.
"The whole weekend felt great from the word go. It's beautiful to win at this legendary track," he said at the podium presentations.
Hamilton, searching for a fourth title and his third with the Silver Arrows team, said he was in damage limitation mode after his wheel spinning start which saw him drop to eighth at one point.
"I did the best I could from where I was and I'm happy with the points. I'll continue to fight over the remaining races," he vowed.
The British-based Mercedes team has dominated F1 since new rule changes were introduced ahead of the 2014 season, and victory in the constructors' category was a formality after opening up an unassailable gap on nearest challenger Red Bull.
Ferrari, expected to challenge more strongly in 2016, lost more ground to Red Bull in the battle for the runner-up spot as Sebastian Vettel and Kimi Raikkonen took fourth and fifth in Japan.
It was the first time Vettel -- who won four world titles at Red Bull -- has finished off the podium at Suzuka since 2009, and his mood was not helped by being held up by back markers in traffic as he battled old rival Hamilton for third.