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.
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Mercedes later lodged an official appeal over the incident, but it was later withdrawn, apparently at the request of Hamilton, although the team later denied this.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.
Daniel Ricciardo, triumphant for Red Bull at Sepang last Sunday, finished sixth, but it was a sorry weekend for the McLaren-Honda pair of Fernando Alonso and Jenson Button, 16th and 18th in the home race for the team's engine supplier.
In a sign of the ever increasing reliability of F1 cars, all 22 from the 11 teams finished the race, with the next scheduled for a fortnight at the Circuit of Americas.
Hamilton clinched the 2015 championship in Texas, but he has an uphill battle to repeat that success with Rosberg, son of 1982 title winner Keke, holding such a big lead.
But Rosberg is warning that it is too early to write off the chances of his teammate, despite a troubled week for Hamilton.
"The Lewis I saw was massively motivated. I can tell you behind the scenes he's as focused as ever," he told AFP. "He always is, especially after a setback like Malaysia.
"I'm well aware of the 33 points of course, but there are still many races to go so I'm just keeping my head down."