Max Verstappen became the youngest Formula One driver ever, taking part in free practice at Suzuka at the age of 17-years and three days.
Hamilton clocked a best lap time of one minute 35.078 seconds to finish 0.240s ahead of Rosberg, who trails him by three points in the championship standings with five races remaining.
Rosberg, who despite suffering a lock-up on a hairpin, was 0.151s faster than Hamilton in the opening session and the day's times pointed to another furious Mercedes duel on the high-speed Suzuka layout today.
"It's been a good day for the team," Hamilton told reporters as the feuding teammates kept up the appearance of harmony in Japan. "It is a tough track for the tyres and we have a lot of work to do.”
Verstappen, son of former Formula One race Jos Verstappen, grabbed the spotlight with his drive for Toro Rosso.
The teenager, who is not old enough to drive on public roads in his native Netherlands, pulled over after 21 laps with smoke billowing from his car.
"I have a problem in the engine," the Dutchman, who will replace Jean-Eric Vergne next season, radioed to his team. "I have smoke out of the engine. What should I do?"
It was a rude introduction to Formula One for the youngster whose entry in the sport has sparked much debate.
"I was not even close to the limit," said Verstappen, who did not run in the second session. "I was just driving safely without doing any crazy stuff."
Finland's Valtteri Bottas was third quickest for Williams in the afternoon, 1.2s behind the Mercedes pair, but ahead of Briton Jenson Button for McLaren and four-time defending world champion Sebastian Vettel in Red Bull.
Meanwhile, Daniel Ricciardo took the blame for a big crash as he slid off the circuit at the final corner while completing his first flying lap of Suzuka's demanding "figure of eight" track. He careered through a gravel trap and hit the barriers with the left front corner of his Red Bull.
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