The German clocked his fastest time of one minute, 32.250 seconds on an overcast afternoon in Suzuka in the second of Friday's two sessions, after having topped the timesheets at the end of the morning.
Rosberg's Mercedes team mate Lewis Hamilton was second in both and although the Briton was 0.214 seconds off his title-rival's pace in the morning, he closed the gap to just 0.072 seconds in the second session.
“It’s been a case of finding my way today,” Rosberg told reporters. “It began with quite a lot of under-steer and we had to work through the setup in order to find a better balance on the car.”
Rosberg extended his advantage over Hamilton to 23 points in the overall standings after the reigning champion was forced to retire 16 laps from the finish while holding a comfortable lead during the last race in Malaysia.
Hamilton heads into Sunday's Japanese round desperately needing to revive his title hopes by clinching a third successive win at the Suzuka circuit.
Their Mercedes team could also wrap up their third successive constructors' crown on Sunday.
“It’s been a really good day with no problems on the car which is great,” said the Briton.
“We managed to get plenty of laps in but there’s still some work to be done overnight in order to find more pace.”
Kimi Raikkonen ended third-fastest for Ferrari, 0.323 seconds off Rosberg's pace, but was unhappy with his car’s balance. The Finn had been fourth-quickest in the morning behind team-mate Sebastian Vettel, who was fifth fastest in the second session.
Vettel heads into the weekend carrying a three-place grid penalty for tipping Rosberg into a spin in Malaysia.
Max Verstappen, sixth in the morning, split the two scarlet cars in fourth.
His team mate Daniel Ricciardo who inherited the win in Malaysia after Hamilton retired, fell to 12th in the second session from fifth earlier after he was forced to abandon his flying lap when the virtual safety car was deployed after Esteban Gutierrez ground to a halt by the side of the track.
The Australian is expecting to leapfrog Ferrari in time for qualifying and the race in what he expects will be a three-way battle with the Italian squad and Mercedes fought out over the remaining races this season.
“If we get the car hooked up in qualifying, we can be strong and can be close to Mercedes and hopefully ahead of Ferrari,” said the 27-year-old.
(Editing by Ed Osmond)
