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 1min 35.078sec to finish 0.240 sec 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 0.151sec faster than Hamilton in the opening session and the day's times pointed to another furious Mercedes duel on the high-speed Suzuka layout on Sunday.
"I was nearly off in the barriers once myself," added the 2008 champion from Britain, referring to a heart-stopping slide where he almost lost control of his car.
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Hamilton has wiped out a 29-point deficit thanks to victories in the last two races and Rosberg's retirement in Singapore two weeks ago.
Verstappen, son of former Formula One race Jos Verstappen, grabbed the spotlight with his drive for Toro Rosso.
"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.